1989 4.0L Engine swapped into 1989 Wrangler

If anyone can give me a hand I would GREATLY appreciate it.
I just replaced my 4.2L engine with a 4.0L fuel injected engine out of a Cherokee. The Cherokee engine came out of an automatic and I have a manual.
Does anyone know anything about the Throttle Position Sensor setup being different for the Manual/Automatic? What do I need to do to make it work?

Thanks for your help!