Now wait...Hmm. I slightly remember a problem like this when I was working in my uncles transmission shop one day. I was only there for a few days doing a carreer study for school, I'm trying to remember what the problem was though. It was on a dodge ram 2500, I'm fairly sure it was the transfercase oil pump, I could be wrong though. You already elimnated the pump though as the problem...maybe your looking at the wrong end of the issue, maybe it's the diff thats the problem and has been a problem with your original drive shaft just you didnt spin the original by hand to realize you had a problem. Just a thought.
DD- 1995 YJ 2.5L, Cat delete, 19lb injectors, 30/9.5r15
Trail Rig- 1994 YJ 4.0L, Rubicon Express 4.5inch lift, 1inch body, D30 Aussie, 33/12.5/r15 Cooper Mud Terrains, front bumper, rocker guards