So I had to realign the clutch disc. Didn't seem like much of anything, but after I got the tranny back in place, and had a friend push lightly, while I rocked the tranny a slight bit from underneath, it just clicked right into place.
Of course this was no earlier that 1:30am..so I left it bolted up to the block and now just have some re-assembly to work on.

Phew, what a pain.

When I first installed the clutch disc, I was a little to lazy and trusting. While laying on the floor, I just set the pilot tool in place and bolted the pressure plate on. This resulted in the disc being just a smidge to low. This time I took my time and used my fingertips to ensure the disc was as centered as I could tell.
This was the trick. Probably also that I moved the tranny in with a little help and little more gently than before.

Now getting the axles back on, the shifter hooked up properly, and the fluid refilled is going to be final tasks.

Thanks everyone for the help/suggestions, I really appreciate it.!!!!