I swapped an NV3550 into a 42RLE equipped 4.0 2004 TJ Unlimited and I have learned a lot. My lessons only apply to these two transmissions attached to a 4.0. I will posit some assumptions based on my experience if you were going the other way but promise nothing. I am doing an engine swap that requires a manual because it uses a different PCM that cannot control the Auto and I don't want to daisy chain the stock Jeep PCM to keep it working. I never cared for auto anyway.
First to dispel some myths: you don't need new driveshafts, the transfer case sits in exactly the same place. If you are using a transmission from the same model run the input and output shafts between the trans and Tcase and between the engine and trans will work.
Big caveat! If you have SKIM, otherwise known as sentry key, quit now! You will need the cluster, SKIM module from the column, keys, ingnition (so you don't have to rekey yours) and PCM from your manual donor vehicle of the same model year. This is prohibitively expensive and as many say in response to the manual auto swap forum threads you may as well sell your auto jeep and buy a manual one. I am doing an engine swap so I quit trying to make the stock stuff work when I found this out, it just aint worth the hassle. SKIM is an unholy bitch. You'll know you have it if you have a grey key. If you have an entire donor vehicle available, go with god, but SKIM is definitely stored in the cluster as well, don't believe anyone who says otherwise. If disabling SKIM was as easy as disconnecting the module and slapping in a $150 used PCM from a Jeep without it, then it wouldn't be much of a theft deterrent. I assume all that is stored in the cluster is an error code to check for SKIM and not the VIN or specific skim codes, so you might be able to replace everything else with SKIM parts from the donor and have it work but probably not. I bought a computer from a salvage donor that definitely never had skim and my key light still came on solid when I tried to start the jeep, yes the SKIM module was removed from the Jeep. I bought another one to double check, throwing more money down that hole. Some companies will claim to remove SKIM, so if your jeep doesn't have sentry key you might get away with buying a PCM from a donor with SKIM and having it wiped. Do NOT plug the PCM in to find out if it has sentry key or it will write SKIM to your cluster and you are effed. You have to make certain BEFORE you turn the key that nothing has SKIM enabled. Reprogrammers who sell rebuilt Computers go by VIN and if yours is for an auto they will send you an auto computer, so you need to find that magic donor vehicle of the same model year, same engine, and either no SKIM or every damn part I mentioned before to make SKIM work. If neither Jeep had skim I assume it would have worked. I promise nothing. Enough about SKIM already!
Things you will need:
A PCM from a manual TJ of the same vintage as yours. Auto and manual PCMs are different firmware and cannot be reflashed from one to another. Likely newer PCMs will work with your jeep but not older ones. Maybe an expert can weigh in on this. I tried to find a compatibility list by model year but never found that info. If you know don't stay silent!
A manual starter. The starters are different between manual and auto. The mounting bols are different too but I made it work with some bolts from the Auto dustcover.
An NV3550 or NSG370 manual transmission. Neither talk to the PCM so you can use either. An AX15 might work too, but if you're going for this swap why not get a newer transmission with ready parts availability that is pretty cheap? Also screw that internal slave cylinder. So I went with the 3550. The six speed would have been cool but the model with the appropriate bellhousing can apparently only be found in 05-06 Wranglers and they are pricey.
Parts for the manual trans that are different from auto and that you need from front to back: Dust Cover, dust cover lower mounting bolts, flywheel, flywheel bolts (these are impossible to find new but there is a GM crossover part I will post later when I find the package) pilot bearing, clutch plate, clutch cover, throw out bearing, (so basically a full clutch replacement kit), fork, that little clip that keeps the fork in place, slave cylinder, hydraulic hose to master cylinder, master cylinder (there should be a block off plate on your firewall that you remove to install this and if you save the nuts off it you can reuse them on the M/C), and a clutch/brake pedal (removing the upper most bolt to replace this involves some gymnastics) In addition you will probably have to source a shift tower and shift handle if they don't come with your transmission. The transmissionmount bracket between the bottom of the transmission and the crossmember / skid plate is different and the bracket that the exhaust hangs onto is shorter becase the manual doesn't have a deep pan like the auto and is therefore slimmer in the belly area.
Things that are the same: the upper and side transmission bellhousing to engine mount bolts can be reused, the nuts and studs from the transfer case to transmission tailhousing will work. If you get a transmission from the same model range the input and output shafts will all work together. They may be different over different years. As I said the transfer case sits in the same place so the driveshafts are the same, at least in my case they are. The crossmember/ skid plate is the same with the same mounting holes and the rubber transmission mount (vibration dampner) is the same.
Accessories: inner shift boot, outer shift boot, shifter knob. And you may need a new tunnel cover depending on year because some have differently sized holes in them. I didn't on my '04. Or you can remove your entire shifter trim setup and install a stock rubber JK shifter boot over the hole, it works!
The auto trans has a massive wiring harness and a half dozen plugs associated with it. If you want to simplify you should source a manual harness to avoid the annoying task of stripping all that out, I just zip tied it out of the way for now. If you are going manual to auto YOU WILL NEED the auto harness which incorporates the wiring for everything fron the firewall back to the fuel pump. Enjoy that mess.
The Auto transmission tells the reverse lights to come on so you will need to wire your own reverse light circuit for the manual transmission, it helps if you source the two pin oval shaped plug for this (likely identical to the one that connects to your transfer case 4wd indicator switch).
In my Jeep the plug for the clutch switch (to tell the PCM it's OK to start the Jeep) was already there. If yours isnt then I think it will work anyway because there is a 20A fuse in space 20 on your glove box fuse panel that tells the Jeep it is OK to start without depressing the clutch (because you have an auto) I can only assume this because SKIM screwed me over and I never got to try.
In short FUCK THIS SWAP. It is possible with a SKIM less ECU (anybody know how to erase that shit from the cluster and steal a Jeep?) but finanacially is not going to be worth it unless you already have a complete donor vehicle in your backyard. (Did you total your manual jeep and the transmission in your auto is trashed? Then sure, do it.)
Me? I thought I'd give it a go because my jeep is beat to hell and I could never sell it for enough money as is to buy a manual Jeep LJ that wasn't also beat to hell. I'm doing an engine swap that won't work without a standalone transmission so I had to pull the perfectly good 42RLE out anyway. I don't recomend it if you are keeping everything else stock.
