360 instal, going on 3 days, need help

Here is how I have always done it.

first, like you mentioned, make sure the shaft fits the pilot bearing....which you say you did so that should not be a problem.

also as mentioned make sure you used a clutch alignment tool so you know thats all lined up.

here is where I always do things different......

I always jack my trans up so the front is angled upward slightly.

then I lower the engine in and I get the engine lined up with the tranny and connected ...and THEN I lower the engine down onto the mounts.

I have done it the way you did before many times....by lowering the engine to the mounts and THEN lining the trans up....I just find it easier having the engine floating in free air when connecting the bell housing because I have freedom of movement and I can rock the engine back and forth/side to side a little if need be to aid in the alignment process.

also make sure all the alignment dowels are positioned with the alignment holes.