Novak Conversions Jeep Wrangler TJ radiator

Intermittent misfire and rough idle (2005 Wrangler X 4.0 Automatic)

RMac80

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Original poster
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Jun 11, 2024
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32
Location
TN, USA
Hi all, I’ve had my TJ about a month now and this forum has been a great help to me so far. Thanks for everyone who contributes good solid content here!

So my TJ has about 104k miles on it. It ran OK when I got it, but it was a little rough feeling/vibration wise. Especially at idle and low RPM, it was the worst when driving and you had to stop at a light with it in gear. Didn’t seem to matter if it was hot or cold. ANother thing it would do, only when hot, was the idle would surge up and down between 800-1200 rpm.

A few days after we got it and had taken it on a few rides, got the flashing CEL on the dash and it was p0301 cylinder 1 misfire. That night, I found your forum and started researching next steps, so everything below was with the guidance of this community!

Round One
-Techron concentrated fuel system cleaner with 10 gallons mid grade 89 octone fuel from a good source (two rounds)
-One full can of CRC throttle body cleaner in bursts as per the instructions (to clean TB itself)
-One full can of CRC throttle body cleaner in bursts at idle through the IACV inlet port as instructed on this forum, until the bursts of CRC did not bog down the engine.
-Cleared CEL codes, did not reset PCM
RESULTS: Almost fully solved the idle surging up and down, restored some power, smoothed out idle considerably.
HOWEVER: Still get very rough idle and sometime 0301 misfire when driving and stopped, seems worse when cold now, but will also do it when warm. Idle surge sometimes comes back when I park it when hot, but it is not as severe.

Round Two
-Autolite XP985 plugs properly gapped and torqued
-Standard Motor UF296 Blue Streak coil rail
-Cleared CEL codes and reset PCM
NOTES: Plug #1 was fuel fouled and had nearly no gap. Other plugs had gaps all over the place. Inspected wiring/connections for coil, was in good shape and the clip even worked well, was not brittle. Inspected wiring for all injectors, and used a listening rod to check for good "click" out of all injectors when running.
RESULTS: Overall ran a lot better, smell of fuel in garage got a lot less prominent, lots more power and greatly improved fuel economy.
HOWEVER: Did not change any of the main symptoms, but they happen less frequently. Still get very rough idle and sometime 0301 misfire when driving and stopped, seems worse when cold, but will also do it when warm. Idle surge sometimes comes back when I park it when hot, but it is not as severe.

Round Three
-Using scanner, did an actuating test on the IACV and it responded smoothly to each setting, no sticking or bogging the engine.
-Smoke tested evap system - no leaks (no codes here but though might as well)
-Actuated purge valve closed with my scanner, verified no vacuum on intake side from canister
-Smoke tested intake/vacuum system. I was injecting smoke from the inlet tube in the air box using a pump up air blocker that came with my smoke system. The throttle body leaked quite a bit around the throttle input shaft, but only when the butterfly was closed. Opening the butterfly allowed most of the smoke to pass through to the intake.
-So I moved my smoke tester to evap canister line that goes into the intake. I found a small leak around the elbow going from the intake to the vacuum accessory harness, so I replaced that.
-Using live data scanning, I looked at bank 1 O2 sensors. upstream fluctuates up and down while downstream decreases to a low value as expected. But the system never seemed to go into open loop mode even after running for 15 minutes.
-Another full overnight cool down, I live data scanned the coolant temp sensor, ambient temp sensor, and throttle position sensor. Temperatures on dashboard gage and in the scan tool all seem correct. Actuating the gas pedal I find the throttle position sensor data to be smooth and not have any jumps or dead spots in the response curve.
-Checked ATF fill level and color, both seem good enough to tell me the transmission isn't starving for fluid and causing my issues when stopped in gear.
-Cleared CEL codes and reset PCM
RESULTS: It has been almost a week with no 0301 misfire code sitting at a stop! But really all I did was replace a vacuum elbow, so I don't trust it...

Current situation:
When cold, it will start easy and idle fine unless I put it in gear, then the idle gets rough. If I drive it before letting it warm up, it will run really rough at a stop in gear. This is when it would sometimes throw the 0301 misfire code. This is the only situation where I ever got the code. Never when moving, never when parked.
When hot, it always starts great, but it sometimes still has rough idle at stop. No codes ever when hot, and not as rough as when cold. Also if it has been driven a while, when I park it I sometimes get a slight idle fluctuation up and down. Not as bad as I did before cleaning the IACV but it is noticeable. If I open the hood when this is happening it all smooths out.

Questions:
1) Does the air leak around the throttle input shaft need to be fixed? I am getting mixed results on that in my research, but if this is fixable it may help my cold rough idle situation...
2) What live data do I need to look at to determine closed vs open loop? I am looking at the closed loop timer and I never see it change when the system should be warm enough. Maybe I am looking at the wrong data or interpreting it wrong...

Next Steps:
I am thinking I need to pull the fuel rail to do the heat soak wrap. Because when it is hot opening the hood makes the issues I am having when hot go away. Mine has injector 3 wrap and a heat shield in that one spot on the manifold from the factory, but it is all in questionable condition. While I'm at it I will probably swap to an older fuel rail with the testing valve, do a fuel pressure test and a leak down test, check all the injectors for leaks. Definitely check wiring pulse with a NOID light since I can do that one cable/connector at a time using my scanner. Probably install new o-rings. Injectors too if these look really bad or I find any leaking.

However, I am not sure any of that will help my issues I'm having when cold...

I have not looked at the MAP or Cam Position sensors yet.

Have not looked at compression, valve springs, or head/head gasket (but my coolant and oil are both clean and levels are staying same). I want this to not be my problem really really badly...

Haven not looked at intake/exhaust gasket. I do not hear any exhaust leak. I do hear a loud hiss on that side of the engine when running but I think it is coming from the throttle input shaft on the throttle body. Maybe I'll do a smoke test in the engine bay and see if anything sucks the smoke in...

I think I have ruled out coolant temp sensor, TPS, O2 sensors, IACV, and evap purge valve based on my diagnostics but maybe not?

Any thoughts on where I should go next? Thanks!
 
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What year is your Jeep? What engine does it have?
Personally, I always fix vacuum leaks first; it's easy and solves a lot of problems.
Heat soak typically won't impact cylinder 1 and only impacts the 4.0L... I'll assume you have the 6-cylinder.
Here are some things I've done to troubleshoot similar problems.
1: Pull the spark plugs and check them; then throw them away and get new ones; I use NGK.
2: swap your 1-3 injectors with 4-6 injectors. If you have the 4-banger, it's all on one bank, so skip this
3: check the wires around the PCM and to/from the injectors and coil pack, make sure none of them are damaged; there are wiring diagrams in the manuals pinned in resources here: https://wranglertjforum.com/threads...ice-manuals-fsm-technical-documentation.4618/
4: Get a good volt meter and check the ohms from each of the wire terminals to each of the respective plugs in the PCM and check for bad grounding (these also ground at the PCM, iirc).
5: Change the coil pack if all the wires are fine and 2 didn't make any impact.
6: Get a bore scope and inspect your valves.
 
What year is your Jeep? What engine does it have?
Personally, I always fix vacuum leaks first; it's easy and solves a lot of problems.
Heat soak typically won't impact cylinder 1 and only impacts the 4.0L... I'll assume you have the 6-cylinder.
Here are some things I've done to troubleshoot similar problems.
1: Pull the spark plugs and check them; then throw them away and get new ones; I use NGK.
2: swap your 1-3 injectors with 4-6 injectors. If you have the 4-banger, it's all on one bank, so skip this
3: check the wires around the PCM and to/from the injectors and coil pack, make sure none of them are damaged; there are wiring diagrams in the manuals pinned in resources here: https://wranglertjforum.com/threads...ice-manuals-fsm-technical-documentation.4618/
4: Get a good volt meter and check the ohms from each of the wire terminals to each of the respective plugs in the PCM and check for bad grounding (these also ground at the PCM, iirc).
5: Change the coil pack if all the wires are fine and 2 didn't make any impact.
6: Get a bore scope and inspect your valves.

2005 Wrangler X 4.0 Automatic (and added to the thread title)

Thanks! I'll have to add the bore scope to my list of things to check I get down past vacuum and fuel system. I assume I would just go in through the spark plugs. Should have done that while I had them out changing them a couple weeks ago...
 
Round 4
-Did en engine bay fog test with the motor running and located the source of my hissing sound, the little vacuum elbow under the map sensor. So I taped it up until I can find a suitable replacement.
-Reading another forum post someone said the PCM on the TJ has a slow data path and the live data in my scanner might have some missing data points. So I went back to testing o2 sensors but instead of all 4 on the same pass I did them one at a time. SURE ENOUGH the bank 1 sensor was frequently dropping to 0.03v so either that sensor is bad or the wiring to it has a short. I will buy a new NTK B1S1 and inspect all the wiring.
-To confirm the diagnosis, I looked at the LONG TERM fuel trim for bank 1 whicn I did not look at before. It was almost at +7% while bank 2 was more like +1.5%. Keep in mind I reset the PCM about a week ago (which I think resets long term learning including the fuel trims).

So if this thing has been running with a bad B1S1 for a long time, no wonder plug #1 was fuel fouled and I was getting p0301 misfires, bank 1 was running WAY too rich. Also now I suspect replacing vacuum elbows did not stop the misfire, it was resetting the PCM which stopped the misfire...

WIll report back.
 
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So I replaced B1S1 with an NTK and replaced the MAP sensor vacuum elbow on Thursday, hard reset the PCM (unhooked battery and touched positive to negative leads) instead of just resetting it with my scan tool.

Actually saw both banks get into closed loop mode and the fuel trims are pretty close to each other for both banks now.

Since then almost all my symptoms are gone! No codes and no rough idle when cold at a stop. I still get a little rough idle at a stop when it is warm.

We took a 3+ hour drive on Sunday with many different conditions. Highway speeds, stop and go traffic, curvy country roads, some washed out gravel (mild off roading). Up and down steep hills. She ran like a champ all day long. No codes, no major issues!

Next step is to replace the remaining 3 original O2 sensors when I get paid again. I'm hoping that wipes out the last little nagging rough idle symptom.
 
I'm hoping that wipes out the last little nagging rough idle symptom.

If you replaced one elbow you probably have more vacuum leaks somewhere. I'd be more inclined to attribute that to a rough idle than the three remaining O2s.

I wouldn't touch them if they're working and it's going into closer loop...not unless live data showed out of range voltages.

-Mac
 
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If you replaced one elbow you probably have more vacuum leaks somewhere. I'd be more inclined to attribute that to a rough idle than the three remaining O2s.

I wouldn't touch them if they're working and it's going into closer loop...not unless live data showed out of range voltages.

-Mac

I replaced two vacuum elbows. The one from the intake to the accessory harness, and the one uder the MAP sensor.

I still have a small amount of smoke coming out of the throttle input shaft on the throttle body when I smoke test the vacuum system but that is all. I've read that it is a difficult fix or requires a new throttle body to fully seal that off. But based on the wear of the o-rings and shaft I have seen on other posts in this forum, I tried turning the throttle a bit and it seals, so this is definitely a vacuum leak that is worse (or only exists) at idle...

Bank 2 upstream O2 sensor is a little bit low on voltage occassionally but not as frequent as the bank 1 upstream was. I am noticing the bank 2 fuel trim creeping up a bit higher than bank 1 over time, though...
 
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I just picked this up for $50 on Amazon. No issues on my 97 but I'm curious to see if I have leaks. Also want to check my 2001 F250.

IMG20240618105107.jpg


-Mac
 
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So to report back, I replaced the remaining 3 O2 sensors and it has been over a month with no misfire codes, drives great!

I do occasionally get some rough idle when cold and stopped in gear. I am going to chalk that up to either the small vacuum leak in the throttle body and/or the fact I cleaned the IAC instead of replacing it.

I am building up parts for a winter project to rebuild the throttle body input shaft o-rings, replace all the sensors and gaskets attached to the throttle body while it's out. I'm also upgrading my fuel rail (to an older one with Schrader valve) and doing the heat wrap/shield kit at that time.

But for the time being, it runs so good we are relaly enjoying it in the nice weather so I am leaving it alone. Thanks to all on this forum who have chimed in and left great content full of wisdom for us to read through and make our TJ experience more enjoyable!
 
When the cold weather hit, my cylinder 1 misfire came back with a vengeance (or it may have been just an issue of time). Flashing CEL and P0301 code came back several time, would shudder and misfire at a stop light again, and sometimes in a parking lot when doing slow maneuvering into a parking lot it would stall out. So in a way it was worse this time than my original symptoms...

Luckily I had been gathering parts for a winter project:

Mopar 4861552AC Fuel Injection Idle Air Control Valve

Got an old style OEM fuel rail from www.fn-jeep.com (the kind with the schraeder valve in case I need to diagnose fuel pressure at idle as my next step)

https://www.designengineering.com/97-04-jeep-4-0l-i6-fuel-rail-injector-cover-kit/ (heat shield/wrap kit from DEI)

UREMCO - 44412 4-8 Fuel Injector Seal Kit, 1 Pack (new o-rings and filter baskets for OEM injectors)

Got some 012 o-rings (to complete this process here
)

FEL-PRO 60948 Throttle Body Gasket

STEP 0) use the FSM procedure to discharge pressure from the fuel system and then remove the leads from the battery

1) Pulled the throttle body and disassembled it, removing the TPS, MAP, and IACV. I put the TB and all the metal parts in a gallon can of the "gunk" parts cleaner dip kit you can buy at Advance or Tractor Supply and sealed the lid.

2) Label the injector wiring for all 6 cylinders before you start, I used masking tape wrapped around each one. Remove the fuel rail and injectors (don't forget to the quick disconnect tool). I pulled the injectors out of the original fuel rail and made sure to number them 1-6 using masking tape on my work bench. Overall the injectors looked decent, just carboned over a bit. Here is a before/after from cleaning them with some CRC and a medium nylon brush.

IMG_7559.jpeg


Injector #3 had a damaged o-ring so it was sucking in dust and grime from the engine bay...
IMG_7558.jpg


3) After removing the o-rings and filter baskets, I cleaned these with CRC and a nylon brush, then reinstalled the new filter baskets and o-rings. I also used a flexible nylon bore brush from a gun cleaning kit and CRC to thoroughly clean the "new to me" fuel rail. I installed the DEI heat wrap on the fuel rail, which needed a bit of modification to accommodate the fuel damper. A little vaseline on the rail side o-rings and I installed the injectors into the rail. NOTE: I swapped injectors 1 and 5 because I am chasing down a cylinder 1 misfire. I chose cylinder 5 because it is on a different bank and on a different firing sequence than #1. That way, if my misfire comes back, or if my long term fuel trim for bank 2 show strange behavior, the problem is following that injector, I will probably buy a remanufactured set.
IMG_7565.jpeg


4) While everything was out, I cleaned the top of the intake manifold where the throttle body goes, removed the old insulation from the intake/exhaust area around cylinders 3 and 4, and ran a shop vac over everything to eliminate dust and debris. Then installed the heat shield (had to pop up the injector wiring cover.

5) A little vaseline on the cylinder side o-rings of the injectors and I reseated the rail, torqued down to spec and reconnect fuel line.

6) Covered the throttle body location on the intake manifold with a shop rag and let the throttle body soak overnight. Next morning I did the procedure in the above youtube video that eliminated the throttle rail/butterfly from wiggling. I made sure to really clean the whole TB with vinyl brush, went back with CRC and the bore brush as needed especially in the air channels for the IACV. I dried it off really good with rags and shop air then reassembled with the new IACV. (Re-used the original TPS and MAP for now)

7) Installed the throttle body with new gasket, torqued to spec, and put everything back together (throttle cable bracket, throttle cables, air intake tube that goes from filter box to the throttle body, etc. (on a related note, the fogger is no longer showing a leak around the TB, so either the gasket or the o-rings sealed that vacuum leak up)

8) Before hooking the battery back up I touched the two leads together for 30 seconds to reset the PCM.

Initial results are promising. It actually will idle all the way down to the lowest line on the tach when not in gear and I never saw it go that low before. It is running pretty smooth. A few long drives and no misfire code. No stalling in parking lots so far. I hope this issue is finally put to bed...
 
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That's one heck of a fine job you've done here. And a darn fine write up to boot. Kudos and thank-you.

By and large this is an excellent example of the path any new owner should follow when there are gremlins. I'll be sharing your thread around.

Tim
 
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That's one heck of a fine job you've done here. And a darn fine write up to boot. Kudos and thank-you.

By and large this is an excellent example of the path any new owner should follow when there are gremlins. I'll be sharing your thread around.

Tim

Thank you for the kind words! All of these steps was just putting together content from several posts around this forum, there are too many good contributors here to mention by name.
 
When the cold weather hit, my cylinder 1 misfire came back with a vengeance (or it may have been just an issue of time). Flashing CEL and P0301 code came back several time, would shudder and misfire at a stop light again, and sometimes in a parking lot when doing slow maneuvering into a parking lot it would stall out. So in a way it was worse this time than my original symptoms...

Luckily I had been gathering parts for a winter project:

Mopar 4861552AC Fuel Injection Idle Air Control Valve

Got an old style OEM fuel rail from www.fn-jeep.com (the kind with the schraeder valve in case I need to diagnose fuel pressure at idle as my next step)

https://www.designengineering.com/97-04-jeep-4-0l-i6-fuel-rail-injector-cover-kit/ (heat shield/wrap kit from DEI)

UREMCO - 44412 4-8 Fuel Injector Seal Kit, 1 Pack (new o-rings and filter baskets for OEM injectors)

Got some 012 o-rings (to complete this process here
)

FEL-PRO 60948 Throttle Body Gasket

STEP 0) use the FSM procedure to discharge pressure from the fuel system and then remove the leads from the battery

1) Pulled the throttle body and disassembled it, removing the TPS, MAP, and IACV. I put the TB and all the metal parts in a gallon can of the "gunk" parts cleaner dip kit you can buy at Advance or Tractor Supply and sealed the lid.

2) Label the injector wiring for all 6 cylinders before you start, I used masking tape wrapped around each one. Remove the fuel rail and injectors (don't forget to the quick disconnect tool). I pulled the injectors out of the original fuel rail and made sure to number them 1-6 using masking tape on my work bench. Overall the injectors looked decent, just carboned over a bit. Here is a before/after from cleaning them with some CRC and a medium nylon brush.

View attachment 573528

Injector #3 had a damaged o-ring so it was sucking in dust and grime from the engine bay...
View attachment 573529

3) After removing the o-rings and filter baskets, I cleaned these with CRC and a nylon brush, then reinstalled the new filter baskets and o-rings. I also used a flexible nylon bore brush from a gun cleaning kit and CRC to thoroughly clean the "new to me" fuel rail. I installed the DEI heat wrap on the fuel rail, which needed a bit of modification to accommodate the fuel damper. A little vaseline on the rail side o-rings and I installed the injectors into the rail. NOTE: I swapped injectors 1 and 5 because I am chasing down a cylinder 1 misfire. I chose cylinder 5 because it is on a different bank and on a different firing sequence than #1. That way, if my misfire comes back, or if my long term fuel trim for bank 2 show strange behavior, the problem is following that injector, I will probably buy a remanufactured set.
View attachment 573533

4) While everything was out, I cleaned the top of the intake manifold where the throttle body goes, removed the old insulation from the intake/exhaust area around cylinders 3 and 4, and ran a shop vac over everything to eliminate dust and debris. Then installed the heat shield (had to pop up the injector wiring cover.

5) A little vaseline on the cylinder side o-rings of the injectors and I reseated the rail, torqued down to spec and reconnect fuel line.

6) Covered the throttle body location on the intake manifold with a shop rag and let the throttle body soak overnight. Next morning I did the procedure in the above youtube video that eliminated the throttle rail/butterfly from wiggling. I made sure to really clean the whole TB with vinyl brush, went back with CRC and the bore brush as needed especially in the air channels for the IACV. I dried it off really good with rags and shop air then reassembled with the new IACV. (Re-used the original TPS and MAP for now)

7) Installed the throttle body with new gasket, torqued to spec, and put everything back together (throttle cable bracket, throttle cables, air intake tube that goes from filter box to the throttle body, etc. (on a related note, the fogger is no longer showing a leak around the TB, so either the gasket or the o-rings sealed that vacuum leak up)

8) Before hooking the battery back up I touched the two leads together for 30 seconds to reset the PCM.

Initial results are promising. It actually will idle all the way down to the lowest line on the tach when not in gear and I never saw it go that low before. It is running pretty smooth. A few long drives and no misfire code. No stalling in parking lots so far. I hope this issue is finally put to bed...

I forgot to mention in step 2 above, make sure you don't leave any o-rings or parts of o-rings inside the cylinder!
 
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