1.5" is a good size gap, about what it would be if you were not getting the input shaft into the pilot bearing. The alignment of transmission and engine (including the angle) have to be correct. If the alignment is off just a bit, it will be very difficult to get them mated up.
With the Bronco, TheBoomBoom and I really were having a difficult time lining things up. We went to the hardware store and picked up some long carriage bolts of the correct thread pitch and size - then sawed off the head. We used these a guides to line things up. It really helped as it pointed out where our angle was off. I didn't need guides when putting the transmission into the FJ40 last month, probably because we had jack on the bottom and hoist on top so it was easier to get the angle correct.
Ricardo Maestas - Bio Page
1999 LX 470, 1971 FJ-40