I didn't see any mention of the pilot bushing/bearing. When you had the transmission out, did you look for the pilot bushing? Rebuilt engines often don't include that bushing. If it is missing, the clutch shaft doesn't have proper support on the crankshaft end and can wobble as it rotates. That can upset the throwout bearing and cause noise even though there is nothing wrong with the bearing itself. Try putting the transmission in gear when you hear this noise, but hold the clutch- if the sound changes, I would suspect the pilot bushing is worn or missing. Some Chevrolet and GMC engines used a ball bearing in place of the oilite bushing, but they are interchangable, and the bushing was standard for decades.
As for transmission and engine alignment, typically you had to disassemble the transmission and bolt the case to the bell housing. I don't remember the procedure, but factory shop manuals describe it. Generally that alignment was not a problem unless there was severe wear on the bell housing or the transmission case. Case misalignment also will cause the transmission to jump out of gear when driving.
Harvester
