Have you put a dial indicator on the crank flange and the bellhousing to check for alignment? If the clutch is centered to the crank center line, its very possible the bellhousing is not aligned and so the trans gets so far in until the alignment mismatch prevents it from going any further. I am assuming you have made up a pair of pins to slid the trans on. A stock trans install is indicative of this kind of misalignment.
Just as an FYI, dial indicating the bellhousing is a big giant pain the the backside, big one, but sometimes a necessary evil.
