depending on the vintage of the engine there shouldn't be too much else to hook up, a few sensors, and the alternator. The trick is finding what you don't need from the wiring in the YJ. Might be easier to get rid of the factory brain.
I used all of my original wiring for the tach,oil, water, starter, alternator and got rid or all the rest. Get a Hanes manual and a test light and have at it. If I remember correctly, I think it is a brown wire that goes to the distibutor from the firewall.