I have a 95 2wd cherokee. I blew the motor and dropped a 4.0 from a 98 into my 95. In the process I broke my transmission so I bought a parts 01xj. I swapped the trans and 4wd from the 01 to my 95 but there are sensors that have nowhere to plug in. What do I do. Swap the harness and computer from the 01 to my 95 ?

A 98 or 01 trans is not going to work right in a 1995 without some work. Start here:
https://www.naxja.org/forum/showthread.php?t=1053970