Is it getting most of the way there then "hangin' up" with maybe an inch or so to go??
If so it's probably just the splines on the driveshaft not in sync with the crankshaft.
I know the unit is heavy so you need a helper. I find it easiest to remove the spark plugs and have a helper move the flywheel by hand once you get the driveshaft up where it belongs but it won't quite engage.
Might be a little tougher since you did this in neutral. If you had of removed it in reverse then moving the prop would have the same effect since the propshaft is "locked up" when in reverse.
Once the splines are lined up it should slide into place.
If you haven't done so you may want to put some high speed bearing grease on the drive shaft splines, just don't get any on the top of the shaft (splines only) - you don't want to cause any additional stress/load on the bottom of the crank - can shorten the life of any number of bearings, but without the grease on the splines, they can freeze into the crank - not good either...