manual swap

Hello!, my name is Karl I live in Quito Ecuador, and wanted to ask from the Jeep guys a question. I live in Quito Ecuador and I'm after a Jeep TJ 4.0L, I found one that is in very good condition but the problem is that it had a transmission swap. If you guys could help me out with some questions...

I have the infamous issue with the 05 and 06 42rle bad shifting because of the bad PCM. Now, because that is discontinued I am looking for an alternate option. Whether that means swapping it for a different engine and tranny combo, swapping it to a manual, or another automatic and get a new...