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You should be able to convert any 91 to 95 4.0L over to a 97 to 99 TJ ECU and harness, but there are some things you'll have to swap out:
fuel rail
sensors
throttle body
etc
Easiest for you would be to get the engine, ECU and wiring out of the same vehicle.
I basically did what you want to do, but in reverse. I put a 97 TJ 4.0L engine in my 1995 YJ, and used all the 95 wiring and ECU.
You'll have to figure out gauges and gauge wiring too. That will likely be more difficult and time-consuming than the engine wiring/ECU part.
fuel rail
sensors
throttle body
etc
Easiest for you would be to get the engine, ECU and wiring out of the same vehicle.
I basically did what you want to do, but in reverse. I put a 97 TJ 4.0L engine in my 1995 YJ, and used all the 95 wiring and ECU.
You'll have to figure out gauges and gauge wiring too. That will likely be more difficult and time-consuming than the engine wiring/ECU part.