I'll try to get pictures up later tonight of this weekend progress. I mocked up the full clutch package and determined I need to shorten the input shaft by about a 1/2 inch. The splines are bottoming out on the bore of the flywheel and preventing the transmission from seating fully.
To make things easier to measure and fully see what the issue was I removed the transmission bellhousing and input shaft. Afterwards I pulled the top cover and tailhousing to inspect the tray of the transmission health. I was presently surprised to get really clean fluid when I drained it, and see what appears to be mint condition shifter fork pads, synchro, and gearing. Like no visible wear of the black nitride coatings or rounding of teeth on the brass synchros.
I then mocked up the input with bellhousing and clutch kit to the block and took measurements of everything. It was much easier to move things and, peek in the bellhousing thru the inspection cover and verify the input bearing was fully seated in the race.
*Notes for me:
Crankshaft counter bore is .823" ID for 1.100", then steps down to about .590 " ID for another .899" of depth.
Input shaft noise is 0.590-.591" in diameter by 0.885" length.
Turning off 0.500" and reducing the shaft to the input nose diameter will allow ~.130 of clearance between the flywheel register and the input shaft.