360 instal, going on 3 days, need help

I would say if you pulled it together with bolts, you have bent the clutch plate.
You are right the plasitc alignment tools are junk.
Or the machine shop did not bore the crank deep enough.
Find your self an old broke trans input shaft, or buy one from Brewers.
Mark it with the depth required and change the disk if any problems with alignment.