Yesterday I decided to do as Roy suggested, to have my lovely assistant turn the out put shaft of the Transmission as I held the 180 grit sand paper on the Input Shaft.
The Flex Disk is still attached to the rear of the Transmission, I placed a 6" long bolt in one of the holes for her to turn the Shaft. makes it easy to turn it at a steady even speed.
Did a couple trial fits and the shaft would sort of go in slightly. then got the brilliant idea to use the Dremel with a 1/4" barrel sander to go around the inside of the Pilot Bearing to slightly open it up. after 3 trial fits, it went right on right up to the adaptor plate.

OH Iam so smart.
Placed the Clutch Disk on with the alignment tool, and then the Pressure Plate. Torqued it all down, and installed the Transmission. HMMM still won`t go the last inch or so to the engine.
Now my thinking is that the Pilot bearing being too large for the crank hole, and forced in, squeezed the outer ring into the Bearings which squeezed the inner rotating Sleeve of the bearing. Also the PB could be slightly out of line (not square) with the flat face of the Crank. the alignment tool lines up the Disk with the hole in the Bearing and the Splines of the tool. then after torqueing the PP and installing the Transmission, my thinking is, that the Splines are slightly out of line with the Disk because the PB is slightly out of line or tilted ever so slightly.
Using the Dremel on the inside of the PB will open it up, but it`s really not a good idea, as we will now have the Steel Input Shaft inside a Steel Sleeve which will not rotate with the shaft as designed. And there could eventually be a possibility of the shaft being galled and a heat build up.
As Roy mentioned up above he used a Dremel..........
I gently used a dremel with 180 grit barrel sander, to clean the crankshaft bore
And Dan mentioned this in his post above.......
I went thru this with my swap and posted it in my build thread. I did the same deal - carefully work the hole in the crank larger with a tootsie roll.
Going with this method, we are talking about one Millimeter of metal between a 85 crank and all the other ones built all over the world since about 1976.
Trying to take off this small amount of metal by hand grinding seems kind of Iffy to my primitive Brain.
My thinking now is to pull the bearing and have a Bronze Sleeve/Bushing made to fit. With the FW now bolted on, my calipers won`t work to measure the Crank hole to get a official size. would have been easy before the FW, but I had it on before driving in the Bearing.
My machinist friend said to bring him the crank and he will machine it to the size, and we both knew that wasn`t going to happen, now if we were building up the engine would be different.
I Tongue in Cheek said "why not fill the hole with JB Weld, slap on the Trans, turn the shaft as it is setting up so not to stick?".
Sorry to be long winded here, just sort of my thoughts as Iam going along here.
Charlie