Trying to get it mostly right the first time: A 5.9 Magnum, 46RE swapped and tummy tucked daily driver TJ

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Dan_Goodwin

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I’ve managed to make some really good progress over the last few weeks (to get back to where I was 2 months ago…)

The first order of business was to free the new engine from the donor truck. A few hours spent on a Friday after work:

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I bought the truck knowing it had a 5.2L in it, but I was in for a surprise! Check out the casting number on the block!

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From here on it was a straight forward deal that I didn’t take many pictures of – old motor out of the Jeep, swap the oil pump, intake and timing chain to the new motor, throw some paint on it and reinstall.

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I got all that done last week, but did learn something in the process…

5.2s are internally balanced whereas the 5.9Ls are externally balanced via the harmonic balancer and the flex plate - or so I thought. The engine had the correct harmonic balancer but no weighted flywheel. Odd. After research I discovered that prior to 1996 Dodge balanced the 5.9L via the torque converter, not the flex plate. I knew this engine had been changed at some point, so I found the casting date on the block to figure out what year this engine is – survey says 3/1994. That means that I should have had a weighted torque converter but since the truck and transmission is a 1999 it wasn’t weighted. I swapped the flywheel over from the old 5.9 and all was good.

My wife was out of town last weekend, which left me and the dog to work on the Jeep. We’re going to the beach at the end of this month and I’m determined to drive the TJ there – that meant this weekend needed to go well. The new motor was dropped in Friday night after work and hooked up for a test fire by Saturday morning. As a recap, the Jeep had started with the Durango PCM but immediately shut down likely due to SKIM or the Security feature (I’ve learned that there’s a difference between the 2 as well). I swapped in the PCM from the donor Ram, turned the key…

And it runs!

(Without shutting off)

I was both ecstatic and relieved to hear it run, really for the first time. I still have to sort out a P0753, P1764 and P0176 trouble codes but I’m guessing that’s related to a wiring issue with the transmission relay circuit I added. The rest of the day Saturday and part of the day Sunday were spent doing the last 10% of a project that seems to take 90% of your time (and really isn’t that interesting to read about).

I went ahead and ordered a new driveshaft from Adams so I can drive the TJ around with the Dana 35 for now. From my research, the 8.8 with a 1350 adapter flange should allow me to re-use this shaft with the new axle. With the new driveshaft in, the TJ moved under its own power Saturday night.

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I have 14 days to get this done (enough) to drive 4 hours to the beach. Game on!
 

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I'm not sure what happens if you do or don't run the correct flywheel or harmonic balancer based on which engine you have. The stroker engine I got has a internally balanced crank but the machine shop that assembled the engine used the Dodge 360 flex plate & balancer. I don't know if it was part of the running issues the OP had with it or not.

Yes the Durango and Grand Cherokee PCM's are a PITA to get to work & as you are learning the SKIM & security are two different things but both will keep the engine from running. Your best option for a PCM is always a Ram pickup from 1998-2000 and is the lower trim levels. While a 1997 PCM will allow the engine to run the gauges won't work.
 

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I'm not sure what happens if you do or don't run the correct flywheel or harmonic balancer based on which engine you have. The stroker engine I got has a internally balanced crank but the machine shop that assembled the engine used the Dodge 360 flex plate & balancer. I don't know if it was part of the running issues the OP had with it or not.

Yes the Durango and Grand Cherokee PCM's are a PITA to get to work & as you are learning the SKIM & security are two different things but both will keep the engine from running. Your best option for a PCM is always a Ram pickup from 1998-2000 and is the lower trim levels. While a 1997 PCM will allow the engine to run the gauges won't work.

It'll vibrate, and you can take out the bushing in the front pump of the trans and or crack the flex plate.
 

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It'll vibrate, and you can take out the bushing in the front pump of the trans and or crack the flex plate.

Could explain some of the issues the OP was having. I bought a 5.2 flex plate for it and a harmonic balancer that doesn't have weights on it. Just seemed really strange that a machine shop would know enough to put an engine together correctly. Now I don't know if the OP gave the shop the stuff and didn't explain about the stroker crank? Just to be sure I had the crank checked when I had all my machine work done and it is an internally balanced crank.
 
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Dan_Goodwin

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Awesome. which radiator and fan combination did you come up with?

My current combo is an ebay aluminum TJ replacement radiator with a Spal 30101516 fan and a Mishimoto shroud I had leftover from the 2.5L. With this combo I have less than an inch to the water pump pulley but could pick up another inch if I cut the threaded portion off the water pump.
 
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Used transmissions are always a gamble and a rebuild should be carried in your budget for a project like this.

Evidently my transmission rebuild is happening...now. Either the torque converter (which is brand new) or the pump in the transmission wiped itself out after the second test drive around the block, which was confirmed by the nice metallic / pearl color in the transmission fluid. It sucks, but its all part of this hobby and dealing with used parts. The plan now is to start selling and scrapping what I can to pay for the new transmission, keep finishing all the little details (that needed to get done anyway).
 
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Dan_Goodwin

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Used transmissions are always a gamble and a rebuild should be carried in your budget for a project like this.

Evidently my transmission rebuild is happening...now. Either the torque converter (which is brand new) or the pump in the transmission wiped itself out after the second test drive around the block, which was confirmed by the nice metallic / pearl color in the transmission fluid. It sucks, but its all part of this hobby and dealing with used parts. The plan now is to start selling and scrapping what I can to pay for the new transmission, keep finishing all the little details (that needed to get done anyway).

I’ve finally taken the time to post some updates to this thread…

I still stand by this previous post that the money for a rebuild should be squirreled away in your project budget, but that doesn’t mean you HAVE to spend that money rebuild the transmission if its not required. My local transmission shop that I have used before was 6-8 weeks out and wanted $1500 +/- for a rebuild and a new unit from Autozone / any online retailer was $2300 and up. Frankly, I didn’t like either of those options.

That’s when I started researching the differences in 46RE overdrive housings - my Ram donor had a supposedly rebuilt transmission (I mean… it drove to the scene of the accident, right?), but it was a 2wd. All my research indicated that the transmission itself was identical between a 2wd and 4wd truck and the only difference is the overdrive housing. I figured it was worth a few hours to pull the pan, inspect the Ram transmission and see if the 4wd OD housing fit.

The PO said this transmission was rebuilt about a year ago and all the signs seemed to confirm that – the date code on the torque converter, socket marks on the pan bolts and the fluid condition. Part of me wishes the transmission was destroyed so the decision was made for me to get a new one, but since I’d (sorta) driven the truck and the internals all checked out I had a decision to make – spend a lot of money and buy new or roll the dice on this used one. I slept on it for a few days and decided to get my monies worth out of my donor truck and go with the used transmission. Fingers crossed this doesn’t bite me later.

I didn’t take many pictures of the swap, but it was fairly straight forward. Remove the old transmission, remove a handful of bolts attaching the OD housing and flush with brake clean (as best I could), flush the cooler and lines with Kooler Kleen, swap the OD housing and reinstall. Easy, right?

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If you ever swap OD housings, be sure to keep everything vertical so the clutches and other wizardry inside the transmission don’t get out of alignment.

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This was the most interesting part of this ordeal. With the transmission on a jack it wouldn’t fit under the TJ and with no transmission in the Jeep the motor was being held up with an engine hoist and a jack as backup. The only way to get the jeep up high enough was to put a floor jack under the front axle (with a 6x6 block for all the safety), raise that as high as it would go while also raising the engine at the same time.

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The rest of the installation went as planned and I had the old trans out, parts swapped and new unit installed over a weekend. Back to where we were 8 weeks ago.
 
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Dan_Goodwin

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With a little momentum on my side it was time to get this build road worthy. This will be a long post as I got all of this done in about a 2 week span in October working entirely in the dark after work since all of our weekends were tied up.

To quote David Freiburger ‘Don’t get it right, just get it running’ is such an accurate statement with builds like this. I needed the kick in the pants motivation that only comes from getting to actually use a rig… I can wire the light bar, transmission temp gauge and other non essential things later.

First step – a new cardboard to-do list. My pictures also get sparse here because much of this was done in the dark after work and most of it is all stuff that’s well documented elsewhere. The mandatory list included:

  • Fix the transmission code
  • Loom and final install the wiring harness. Protect from melty or spinny things.
  • Install rear upper control arms, bump stops, track bars and rear track bar relocation bracket
  • Install air intake
  • Install coil spring spacers (until proper springs can be ordered).
  • Fix brake light switch
The P0753 Shift Solenoid A transmission code was first on the list. My hunch was something was wired incorrectly on the relay I added so that’s where I started due to the fact that the code remained after swapping out the PCM and transmission. I verified the wiring was correct and started checking resistance across wires to verify I didn’t have any bad connections. The problem ended up being the Transmission Control Relay Output wire had pulled out of the terminal and was not making a connection. I re-crimped a new terminal and boot on and crossed this issue off the list

I also now have an intermittent issue that occurs when I plug in my code reader that the speedometer goes nuts and the reader will no longer will connect. We’ll figure that out when it becomes consistent.

The harness was loomed with stuff I bought off Amazon and taped with 3M Super 33 electrical tape. I tried to copy the same method that Chrysler used that wrapped the wires then wrapped the loom to lock it all into place. I’ll go into more detail in the wiring post once I have that completed.

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The Savvy rear control arms were installed and pinion angle set. As of this post, I have not installed the rear track bar and relocation bracket yet. That should happen within the next week.

I’d originally picked up a ZJ air hat to tie into the stock TJ air box but due to a tab on the throttle body and notches in the hat, it can’t be clocked correctly to point to the TJ air box without modification. For the time being I slapped a parts store cone filter on the ZJ hat.

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The front Currie track bar was installed and I did run into an issue where the grease zerk interfered with the axle mounting bracket. Some massaging with the die grinder and carbide burr fixed that issue.

Next was to address the front springs and bump stops. The factory bumpers had long since left the chat from dry rot and the Rough Country springs were nowhere near up to the task of keeping the new found weight of the 5.9L suspended. If it’d had bump stops, it would have nearly been sitting on them. I went cheap and reliable for the bump stop setup, which consists of Crown OEM replacement bumpers and 2 hockey pucks per side to keep the tire out of the fender. The final combination on the springs ended up keeping the RC 2.5” springs and adding a 2” spacer to them. Do I recommend this for long term use? Nope. But this combo did give me the correct ride height, provide a surprisingly good ride quality and most importantly got the Jeep on the road.

01d772d1d7964354ddf2427484ea2aba36f8914bf8.jpg


Lastly and pretty importantly was fixing the brake light switch. On the TJs, the throttle, brake and (if equipped) clutch pedal are an assembly that is mounted to the firewall with 4 bolts. Without a doubt the worst part of this build was swapping the pedal assembly from the manual to an automatic setup I ordered off eBay. I pulled the driver seat, laid down some blankets and just made it happen. It was all kind of a blur and I’ve tried to forget the rest of that experience.

If you’ve ever looked at the brake light switch on the TJ, it sits against the brake pedal and is pushed to a normally open state. When the pedal is pushed and takes pressure off the switch, the brake lights come on. I swapped the brake light switch from the manual to automatic pedal assembly and reinstalled it only to find the new pedal stops short of the switch, meaning the switch is always closed and leaves the lights on. The temporarily permanent solution? A zip tie. I cut the tag end off flush with the head of the zip tie and positioned the head to make contact with the switch. It’s not dumb if it works.
 
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Mike_H

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With a little momentum on my side it was time to get this build road worthy. This will be a long post as I got all of this done in about a 2 week span in October working entirely in the dark after work since all of our weekends were tied up.

To quote David Freiburger ‘Don’t get it right, just get it running’ is such an accurate statement with builds like this. I needed the kick in the pants motivation that only comes from getting to actually use a rig… I can wire the light bar, transmission temp gauge and other non essential things later.

First step – a new cardboard to-do list. My pictures also get sparse here because much of this was done in the dark after work and most of it is all stuff that’s well documented elsewhere. The mandatory list included:

  • Fix the transmission code
  • Loom and final install the wiring harness. Protect from melty or spinny things.
  • Install rear upper control arms, bump stops, track bars and rear track bar relocation bracket
  • Install air intake
  • Install coil spring spacers (until proper springs can be ordered).
  • Fix brake light switch
The P0753 Shift Solenoid A transmission code was first on the list. My hunch was something was wired incorrectly on the relay I added so that’s where I started due to the fact that the code remained after swapping out the PCM and transmission. I verified the wiring was correct and started checking resistance across wires to verify I didn’t have any bad connections. The problem ended up being the Transmission Control Relay Output wire had pulled out of the terminal and was not making a connection. I re-crimped a new terminal and boot on and crossed this issue off the list

I also now have an intermittent issue that occurs when I plug in my code reader that the speedometer goes nuts and the reader will no longer will connect. We’ll figure that out when it becomes consistent.

The harness was loomed with stuff I bought off Amazon and taped with 3M Super 33 electrical tape. I tried to copy the same method that Chrysler used that wrapped the wires then wrapped the loom to lock it all into place. I’ll go into more detail in the wiring post once I have that completed.

View attachment 380957

The Savvy rear control arms were installed and pinion angle set. As of this post, I have not installed the rear track bar and relocation bracket yet. That should happen within the next week.

I’d originally picked up a ZJ air hat to tie into the stock TJ air box but due to a tab on the throttle body and notches in the hat, it can’t be clocked correctly to point to the TJ air box without modification. For the time being I slapped a parts store cone filter on the ZJ hat.

View attachment 380958

The front Currie track bar was installed and I did run into an issue where the grease zerk interfered with the axle mounting bracket. Some massaging with the die grinder and carbide burr fixed that issue.

Next was to address the front springs and bump stops. The factory bumpers had long since left the chat from dry rot and the Rough Country springs were nowhere near up to the task of keeping the new found weight of the 5.9L suspended. If it’d had bump stops, it would have nearly been sitting on them. I went cheap and reliable for the bump stop setup, which consists of Crown OEM replacement bumpers and 2 hockey pucks per side to keep the tire out of the fender. The final combination on the springs ended up keeping the RC 2.5” springs and adding a 2” spacer to them. Do I recommend this for long term use? Nope. But this combo did give me the correct ride height, provide a surprisingly good ride quality and most importantly got the Jeep on the road.

View attachment 380959

Lastly and pretty importantly was fixing the brake light switch. On the TJs, the throttle, brake and (if equipped) clutch pedal are an assembly that is mounted to the firewall with 4 bolts. Without a doubt the worst part of this build was swapping the pedal assembly from the manual to an automatic setup I ordered off eBay. I pulled the driver seat, laid down some blankets and just made it happen. It was all kind of a blur and I’ve tried to forget the rest of that experience.

If you’ve ever looked at the brake light switch on the TJ, it sits against the brake pedal and is pushed to a normally open state. When the pedal is pushed and takes pressure off the switch, the brake lights come on. I swapped the brake light switch from the manual to automatic pedal assembly and reinstalled it only to find the new pedal stops short of the switch, meaning the switch is always closed and leaves the lights on. The temporarily permanent solution? A zip tie. I cut the tag end off flush with the head of the zip tie and positioned the head to make contact with the switch. It’s not dumb if it works.

You have to reset the brake switch to the new brake pedal. Its detailed in the service manual. I think they just get pulled apart, and then you press the brake to "reset" the position of the contactor, but look it up. Its not hard, its just been a while since I've done it and I don't remember the details.

Edit: YouTube University to the rescue!

 
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Dan_Goodwin

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You have to reset the brake switch to the new brake pedal. Its detailed in the service manual. I think they just get pulled apart, and then you press the brake to "reset" the position of the contactor, but look it up. Its not hard, its just been a while since I've done it and I don't remember the details.

Edit: YouTube University to the rescue!


Awesome. I had no idea. Thanks!
 
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Wildman

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The P0753 Shift Solenoid A transmission code was first on the list. My hunch was something was wired incorrectly on the relay I added so that’s where I started due to the fact that the code remained after swapping out the PCM and transmission. I verified the wiring was correct and started checking resistance across wires to verify I didn’t have any bad connections. The problem ended up being the Transmission Control Relay Output wire had pulled out of the terminal and was not making a connection. I re-crimped a new terminal and boot on and crossed this issue off the list

Are you talking about at the PCM plug or at the transmission plug? I've got the same code but the only thing common on mine is the PCM. I vaguely remember having this code on my old transmission with my old wiring harness. So right now, my PCM seems like it might be it, but I'd loaned this to PCM to someone else and he never mentioned having this code. I've got to try and trace it down at some point, but I've got a while before it's a needed thing.
 
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Are you talking about at the PCM plug or at the transmission plug? I've got the same code but the only thing common on mine is the PCM. I vaguely remember having this code on my old transmission with my old wiring harness. So right now, my PCM seems like it might be it, but I'd loaned this to PCM to someone else and he never mentioned having this code. I've got to try and trace it down at some point, but I've got a while before it's a needed thing.
The plug in question is one in between the PCM and transmission (formerly the C103 and C104 on the TJ and C105 and C106 on the Dodge). I spliced in a common Delphi plug to make the TJ body harness marry up to the Dodge engine harness and that's where my issue was.
 
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Paparock1

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Dan is that your TJ air conditioner compressor? My lines were different for the Grand Cherokee and my TJ is why I ask. My TJ compressor wasnt really a direct swap
 
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That's the Ram compressor and a line set off a 1996 V6 Dakota (UAC HA111284C ) I'm still working through the AC system (really, its down to fitting the drier / accumulator) and plan to give a parts list once I get it figured out. The drier / accumulator is a tight fit and I'm trying to use all OEM parts without modification.
 

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OK these aren't my A/C setup but they are how others have done it. This first set was all custom made lines.

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My donor was a durango and I was going to use that compressor but it had 250,000 miles on it and I didn't even know if it worked. I ended up buying a new 5.2 ZJ compressor, suction, and discharge lines. I have the lineset from the durango and it's very different from a ZJ lineset, but I heard the ZJ used the same fittings as a TJ. They didn't. The ZJ dryer has it's lines welded into the dryer with hoses lengths that are all wrong for the TJ stock drier location. With the tube fenders I run and the headers I run I had very little room to work with. I ended up using the stock liquid line (firewall to condenser). I used a stock TJ dryer with its mount modified to move it as close to the battery as possible as to not hit the header, I used the stock line from the dryer to the firewall (the short one) and bent the line to shape as needed to work. Now, here's where the ZJ lines kinda work but not really, the high pressure line from a ZJ obviously bolts right into the port on the compressor but the end that goes into the condenser had a female end on it. The TJ condenser fitting is also female. I had the old lines from the TJ so I cut the male end i needed off and had it tig'd onto the ZJ line. 3 out of 4 lines done. Onto the low pressure line. Being that I needed to use the ZJ line again to bolt onto the compressor and it's line was welded into the ZJ dryer that i can't use, I again had to incorporate the TJ line on the dryer side, with the ZJ line on the compressor side with a tig welder. Thank goodness the lines are fairly soft aluminum and rubber hose because it took a lot of massaging to get them to route/look right. I'll have it vacuumed and charged this week and I should be good to go!



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Wildman

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And on the hat for the throttle body the Dodge pickup hat has the notch to go towards the stock air box.

IMG00806[1].jpg


Then I'd tried to add a piece of tubing to route it over the fender more.

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Then had this setup for a while that was made for the Grand Cherokee with a V-8.

IMG_7127.JPG


I can't find the pictures of it with the washable dry filers on it. None are great but if you have the room stock is best.

IMG_7128.JPG


One member over on Jeep Forum made this setup. He's selling it now because he'd decided to go with something else.

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If I remember correctly this is from a Dakota but I'm not positive.

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These Jeep air cleaner assemblies are becoming hen's teeth. And I had one a sold it for CHEAP not too long ago.

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With the ‘Mandatory’ list completed, a thorough once over and fresh fuel in the tank it was time to drive this rig. The first break in run was to one of our favorite ice cream shops. I was as nervous as I was excited.

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The trips progressively got further away from the house as I gained faith in my newly built contraption. This was the first 40 mile round trip to work.

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All the hours spent researching and wrenching on the Jeep have paid off in spades as I’ve put 300+ miles on this build to date with no real issues to speak of. I really think I got this mostly right the first time and I owe that in no small part to all the knowledge on this and numerous other forums. This engine and transmission combo work so well in the TJ this really should have been a factory option as the 5.9L has enough power to make the Jeep nimble and fun to drive, but not stupid or out of control. I still have a lot to finish and I’ve already come up with a lengthy list of things I want to change, but getting to enjoy this build has me more motivated than ever to keep working away at it. Here are my initial thoughts and things to fix:

  • The speedometer is shockingly close to accurate as-is. A Speedohealer might be added at some point to make it perfect. (Probably not)
  • I’m not convinced the fuel gauge is exact yet. I think its reading lower than what’s actually in the tank (which is the better than the alternative).
  • This thing is a BLAST to drive.
  • The exhaust sounds phenomenal, but it hits a brain rattling exhaust note around 2700 RPM. Fine for a trail rig, but not so fun at cruising speeds. The tailpipe is also touching the trailer hitch which will cause a snowball of a project. I have a hitch hauler and a small utility trailer I put behind the TJ fairly often, so I need to retain a hitch of some kind. To change the muffler I really need to ditch the hitch, raise the entire tailpipe up and install a new bumper at the same time.
  • The radiator and fan have had no issues keeping it cool thus far.
  • Current MPG is 9 +/- and should really be better than that. My driving has been… spirited, but not THAT bad.
  • I’m getting some driveline vibrations so the pinion angle must not be perfect.
  • The track bar is rubbing the gas tank skid plate.
  • The oil pressure is reading lower than I’d like at idle.
I’ve ordered some Core4x4 lower control arms to properly set the pinion angle and hopefully give the track bar some clearance. I’m planning to spend a day wrenching on the Jeep I can catch a semi warm day over Christmas.
 

Wildman

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Awesome, glad you've got it running and driving.

9 MPG even with your foot in the floor is lower than I'd expect. Have you checked for codes? The other thing to do is check your PCM numbers for the Death Flash list.
I am in total agreement that they should have offered a V-8 in the TJ.
Will a bumper with a built in hitch work for you? I have a cargo trail that I pulled behind mine also and had a bumper with a hitch but you do have to be careful if you do get one that it has the clearance behind it to get the stinger in or modify one that is for your Jeep only.