It can sometimes be very difficult to get the trans in all the way even when they are aligned almost perfectly.
I had similar troubles while changing the clutch in a '93 F-150 with an M5R2 5-spd, probably the same transmission. It has an integral bellhousing, and when in the trans tunnel it was a tight fit with no wiggle room. Not to mention, the dowel pins were extremely tight, and the input shaft seemed like it would NEVER go in.
I ended up getting it aligned correctly, and then using several C-clamps around the bellhousing to gradually pull it onto the dowel pins and insert the input shaft. It worked like a charm, and after it was on far enough, the bolts were able complete the job.
All it took was a little ingenuity. If the trans is not integral with the bellhousing, DO NOT attempt to pull the trans on by tightening the bolts. You will break the ears off the case.