Question...the input shaft...is the tip of it cut off flat and straight, or are the edges chamfered? With 1/2 inch to go, you are most likely not hitting the hole...just a 1/32 off will jam you up. You can take a flap disk and break the leading edge a hair. Just go evenly all the way around...maybe a 1/16 chamfer or so.
On the bolt thing...snug it up, and 'wiggle' the trans, then snug up more....if you crank the bolts down, and the input shaft isn't dropping into the pilot bushing, you'll probably just deform one edge of the pilot bushing and that'll lock you out. Doesn't take much of a "dent" along the rim of the pilot bushing to jam you up.
Worst case, don't be a gorilla and force it by cranking down on the bolts...bust an ear and you've really screwed up.
You did set up he clutch with an alignment tool, right?
