Car: 1991 Civic Hatchback DX, 260K miles, 5-speed manual transmission.

Hi Scotty,

This is a follow-up question after going thru your feedback from my initial question.  Here's a review of what I have done so far.

I removed the manual transmission to replace a noisy input shaft bearing.  While the tranny was out, I also replaced the following:

Clutch and flywheel, throw-out bearing, rear main seal, distributor oil seal, and all rubber seals on the tranny housing.

Anyway, I took your advise and went thru the whole process, again - removed everything , checked to make sure the clutch was installed correctly (which it was), checked everything else, including the starter to make sure it's good.  After installing everything back, I turn the key and I get the same result:

The engine is cranking for about 4 seconds and then, a noise like something is hitting inside, like a thud.  And it repeats with cranking for about 4 seconds and the thud-like noise.  With that, I removed the plugs and turn the engine counter-clockwise.  I did not hear anything hitting or a thud-like noise, but you can feel more resistance at certain point of the turning circle (if that makes sense).

I also removed the starter and have it tested at Autozone and according to their testing machine, it's good.

The car was working fine before this whole process except the annoying noise from the input shaft bearing.

I don't know what else to check at this point so any help would be greatly appreciated.  Thanks