I usually pull the whole thing, trans and all. But that's just me. I remove as little as possible, pull the front clip, and slide that monster out. I like it a lot better tearing everything apart on a stand or the floor rather than in the Jeep.
'86 MJ 2.1L 4x4 MT LWB - Factory Diesel
'87 MJ 4.0L 4x2 AT LWB - Metric Ton
'97 XJ 4.0L 4x4 AT Country