Where are you in Ontario? If you're close, I have all the tools to check alignment.

The bearing retainer is a snug fit in the bell and often needs to be twisted and coaxed in. Also, the trans has to go in straight - best accomplished with some long bolts with the heads cut off installed in the top two holes in the bell.

Have you got the clutch disc in backwards? It installs one way only. If installed backwards the slines on the input shaft will bottom out before its all the way in. Just using an input shaft is no indicator that things are "right". It still may not be going in as far as it has to.