Welcome to the YJ madness.
I still have a 75% modded stock YJ engine harness setting here on the floor to go in mine. I am setting it up to run off a 1227727. I just have so much going on lately I have not had time to finish it up.
The stock 4.0 system is really not a bad system. There is just no aftermarket support or tuning for the ECM. (the OBD1 ecm's that is)