Wade,
As to your noise problem, I think I might have had the same issue. I finished putting the XJ back together last night and went for a drive, and everything ran fine. This morning when I left home in the XJ, I noticed this random thumping noise. It felt like is was coming through the floor and I could "feel" the thump with my feet. It started doing it while I was sitting still and also moving at low speeds. Then I got on the freeway and would hear it a bit every time I went over an average bump.
I started thinking about what it could be, and I thought about the crossmember bolts. Specifically the 4 nuts that you put up inside the center part of the crossmember, going onto the bolts that hang down from that rubber tranny brace or whatever it is. I remembered that I torqued them before removing the jack stand that was holding up the tranny, but I never re-torqued them after "lowering" the tranny back to rest on the crossmember.
So I torqued those bolts with a regular socket wrench, and that improved the noise. When I got back home an hour or so ago, I grabbed the torque wrench and torqued them some more, up to about 35-40 per bolt. Then to be safe I re-torqued the main crossmember bolts and nuts on the edges to about 35-40 as well. The thumping sound has completely disappeared from what I can tell. So based on that I believe that the tranny might have been just a tad loose, and it was rocking up and down just a bit over bumps.
Did you re-torque those x-member bolts after removing whatever you were supporting the tranny with? Is this even the same issue you are having?
Hope this helps.