Been on this forum too many times to count trying to find some answer to my transmission woes on the TJ. I've learned something every time and these posts have been invaluable to me. So hopefully I can be a help to all you other jeepers out there. This has been a 2+ year ordeal that had progressively gotten worse with transmission slippage, a multitude of OBDII codes and dozens of hours of frustrating work and missed fun on weekends trying to figure this out. I had been blaming all my problems on the 42RLE that has 124000 miles on it and was about to get one from a scrap yard and this only after I traced all the wiring from tranny to PCM and power dist center. Changing transmission fluid and filter twice in a year while removing valve body and taking out and cleaning TRS TPS input and output speed sensors.Everything I could find on the transmission. The only thing was after I would disconnect the battery my Jeep would run perfectly until the devilish computer had a chance to relearn its evil ways. Then my CEL started throwing the dreaded U0101 (TCM not communicating with PCM) and P1603 (one of those arbitrary,vague codes that the Jeep/Chrysler techies must have fun laughing at us trying to figure out). Every thread I've ever read on this and other sites pointed to a new computer only there aren't any of my specific models out there. So now I'm totally stuck! Jeep goes into limp mode after 10-15 miles after disconnecting battery all night and this has become my daughters only mode of transportation. So... I made myself go back to square 1 and started looking at this as primarily a PCM/TCM issue which is EXACTLY WHAT IT WAS!!!!!!!!!! I had read a post sometime earlier in my quest that dealt with removing the PCM and taking the circuit board out and resoldering the "pads". But that was for an older XJ, i think, and quite frankly scared me. I have 0 experience working on any kind of microelectronics and didn't want to risk fooling with that. Fast forward to Monday night 4/18/2016 and in my frustration I decided to pull the circuit board out to see what I could see. I researched the PCM post again and went to FRYs electronics to purchase the DeOxit, 30watt soldering iron, and the proper Rosin core solder. While i was looking around for the DeOxit an older, very kind gentleman asked what I was going to tinker on. I ended up sharing my whole story with him. He told me about a product called PureTronics and that it was just as good as DeOxit and then proceeded to inform me that he was a retired electrical engineer and that he'd be happy to give me his phone number and talk me thru the fix once I got home. So we exchanged numbers and off I go feeling more confident and hopeful than I have in months. I get home and immediately pull the PCM then called my new hero. He told me what to do in these exact steps.
1) clean the outside of the unit and the PCM plugs with QD electrical spray before i even take off PCM. Make sure it's not dusty or dirty. Oops.
2)remove torx screws and spray screw holes with QD spray
3)remove PCM black cover gently be very aware of contaminants that may
have tried to sneak in. I have no idea what the gel is called that is in the PCM but I know that it works actively against you from this point on.
NOTE: it will be best to perform this with new, anti static gloves
4)this was by far the most difficult part. Gently begin to pry up circuit board. It is unbelievably difficult to do. I was able to use a piece of a split drumstick to get to the very edge of the board, being careful to not touch any of the copper trace or circuits. It took a long time to get this out. The gel is strong and is pulling against you the whole time. I eventually got the board up enough to get another drumstick wedged between the board and PCM casing. Then I was able to slowly roll the stick for maybe an inch or so at a time to hold board and let the gel release. Finally after 15-18 minutes or so I finally got Circuit board out. I was very apprehensive but I was ALL IN at this point.
5)gently remove gel from the pin sites where you can see the little solder joints where pins meet circuit board. I used a #10 blade scalpel(I'm an RN in the OR). I tried my best not to touch the board with the blade and was able to keep the piece of gel mostly intact so I could put it back on after I was done.
6)So now I'm at the mercy of my new friend on the phone and he asks me if I see bad solder, a broken pin site, corrosion, contamination or any other suspicious thing. I tell him I have absolutely no idea what any of those things look like on the microelectronic level and that I'm definitely not comfortable trying to solder anything this small even if it is broken. He tells me to very gently rub with my gloved finger or thumb the rest of the gel off of the pin solder sites. I did. It was very obvious after this what was going on. The gel is very clear/transparent. As I started gently rubbing the gel off the solder the gel all turned brown!!!! He told me that is corrosion on the micro level. Oxidation on the back of the pins!!!! I got my large Magnifying glass and could see what looked like little brown freckles on the solder.
7)Using a new tooth brush gently clean/remove the rest of the gel remnant on the pins and also on the closest surrounding components as they could very well have some contaminant on them because of proximity to the pins. I did each of the four plug- 32 pin sites the same way.
8)This is when the magic happened!! He then told me to hold the board upright and quickly spray 2 very short sprays of PureTronic on the exposed pinsite solder joints and the microcomponents. WOW!!!!!!!!! in less than a second all that metal turned from dull to freaking BRILLIANT, SHINY, New looking metal!!! I've certainly never seen anything like it. And that was my fix!!!
9)Put the circuit board back in the casing making completely sure that the gel is covering EVERY SINGLE part of board. If it doesn't you can gently massage the gel to cover up uncovered pieces. It's not difficult at all. If you have any uncovered areas or contaminated gel that you don't feel comfortable reusing. He said you can use a very small shot of clear,silicone caulk.
*NOTE* You must get the cover on and make sure you push it down hard enough so that the plug ports are our far enough to receive the harness plugs completely. If not they won't snap on.
10)Spray all Torx screws with PureTronic/DeOxit whichever you prefer to use. Also spray in the screw holes of PCM. Make sure to get the long screws very clean and oxidation free before you reattach to firewall.
11)spray inside harness plugs with PureTronic and let dry. Then reconnect PCM.

I can honestly say that when I started my/my daughters JEEP IT HAS NEVER RUN AS GOOD!!!!!! My transmission shifted smoother and responded quicker than it ever had. EVERYTHING seemed better. Faster start on ignition, brighter lights, more responsive breaking. I mean EVERYTHING! I put over 50 miles on it that night. Running it hard on hwy. On a few trails. and thru a couple big ditches. lots of off/on starts and getting into passing gear then slowing down and going thru all the gears/shifts again. It's now Wednesday. My daughter has taken it to the beach and had blast for the first time. I truly believe that she is in a safe, dependable vehicle now. And I pray that my efforts can help all of y'all. I believe we should all do this as a PM after maybe 5-6 years or 80000-90000 miles. I will also admit I was ready to blame ALL MY PROBLEMS on the 42RLE but it is performing incredibly as of now!!!!!!
Good Luck and Keep the rubber side down!!!!