Thrust Bearing- Abnormal Wear

I just got back from vacation. Here are some belated responses to some excellent questions.

The transmission input shaft measures 8 9/16" to the surface that bolts to the bell housing (picture attached).

I don't know if the crankshaft (No. 2532457- P4R10) flywheel flange is correct for a 4 speed (picture attached). The far end of the inside of the flange doesn't look rusty, but the end of the input shaft doesn't look worn. It's hard for me to tell if the input shaft is hitting. I can't put the input shaft into the crank flange yet because the short block is on an engine stand, until I take it off to deliver it whole to a machine shop.

I should also mention that I discovered this issue when I pulled the trans to replace the LUK clutch and pressure plate that I installed last summer. The clutch pushed in hard at the top and easy after that, which made it difficult to drive on the street. I put about 1,300 miles on this setup.