So i just go my transmission for the third time now and it was just as fun as always, however i didn't find what i expected. After getting the pressure plate and clutch disk off i noticed the nipple on the end of the transmission input shaft had surface rust on it. Thus it couldn't have been properly seated in the input bearing. I grabbed and alignment tool supplied with the clutch kit and shoved it in the bearing but it was loose and the bearing looks brand new.

I noticed the clutch kit comes with two guide tools and bearings, same spline but different diameter nipples. I must not have realized to swap the bearing when i swapped transmissions awhile ago.

Can anyone think of any issued that could be related to the input shaft of the transmission effectively not having and input bearing to support it, noises, damage, etc? I am finding a pilot bearing puller tomorrow to swap it but i am curious if this could be one of the elusive clunking noises that drive me .