Is there a way to disable the transmission part of my ECM on my ZJ, so I can install a different Tranny. I don't care about the CPS, I will have that machined into the bell.
Nope. XJ got AW4 and ZJs got the Mopar trans with controller (except early '93 which got the AW4) I think you swap to a std trans computer and you're good to go, but I'd ask on the HO EFI thread on Yahoogroups (I'm on the Renix EFI one where some guys are trying to hack the system to do upgrades)