Funny how this seems to be an ongoing forum discussion elsewhere too.. I have never had problems installing a manual but did with the last time installing my new TKX on my mostly stock Explorer 302 while it was out of the car..
I had fit the pilot bearing and the clutch disc on the trans so I knew they fit.. Had my neighbor guy over to help and we still could not get it on..
Someone sells an alignment tool ( I think it was Hanlon's) that the pilot area is a couple of thousandths larger in Diameter so it is more " precise".. I ordered one and it did not make any difference.
What I ended up doing was attaching the bell housing to the transmission ( the fork and TO bearing were on it) and it slid right on.. Not sure why, but the two bellhousing dowels on the block were a great guide when doing it this way..