RESOLVED:

In the past, I've been able to get other manual trannys
to mate together with the bell housing a bit easier than
this one, but it's now fully seated and I feel a lot better.

In the end it was my mistake (shocker). I used slightly
longer bolts to pull the to units together, as the gap between
the Trans and housing was to big to use the stock length bolts
for this purpose....so the longer bolts were simply bottoming
out in the bell housing making it feel as though the input
shaft was not engaging properly or worse too long for the
crank.

To resolve the issue, I used washers on the longer bolts so they wouldn't bottom out and they pulled the two units together enough that I could trade them out for the stock length bolts.

Thanks to all replys and suggestions. I either have a 4speed crank or some auto cranks do have enough cavity built into them for the input shaft.