mine is a little different scenario but I did use a YJ harness when I did a 2.5L to 4.0L swap. but mine was all plug and play. No splicing required. I have a '95YJ that had the 2.5L in it and I used a '94 motor took about 2 weeks to get running again runs and works great.
1993 Jeep Wrangler
4.0L Tom Woods rear HD shaft
D30 w/yukon alloys, lock right, jb4x4 bracket, Rusty's HD tie rod 8.8w/ LSD,SOA xj rear 100" wheelbase, homemade greasable boomerang shackles, SS braided lines, 1" prothane body lift, 35" TrXus M/T, smitty built XRC.
lots of gen right armor and rear stinger.