I think its the computer side of things thats going to give you head aches. The TJ's PCM is going to always be looking for input from the TCM. I know there are ways around this and I think it involves finding a PCM from another 2003 TJ only manual. I believe the Cherokee trans was a little longer than the 42rle. I hope someone else can give you more detailed info,
"That's awesome advice. Anytime I have a difficult repair, I fix something else that's much easier to get to. This one time, there was a hole in the oil pan so I replaced the side mirror on the driver's door."
Wanted: Tuffy rear underseat drawer. PM me if you have one.