Re: trouble reinstalling a bottom end
If you leave the lower unit in forward, make sure the shift shaft remains properly positioned. When in fwd gear the shift shaft has about 270 degrees of free movement and there's only one correct position to reinstall. Spin the shift shaft CCW with pliers etc (cushion the jaws with tape to prevent damage to the shift shaft splines). When you feel a resistance it's about to shift into Neutral. But don't go so far as to shift to Neutral, leave it in this maximum CCW position while still in Fwd.
At this position, if you look at how the reverse lockout rod sticks out of the exhaust tower, you'll see that it will point to the middle of the ramp on the shift cam. If you haven't pulled the shift cam off the shaft (and no one has messed with it prior), it'll already be in the correct position.
Something else that'll cause a hangup is the rubber gasket for the exhaust tube. It should fit solidly against the inner walls of the gearcase, if it's bowed-in, it'll bind on the exhaust tube. Spread a thing coating of grease on the lower part of the exhaust tube, where it slides into the gasket.
Make sure that the plastic guide sleeve is in place in the upper water pump housing. This sleeve is what first catches the copper water tube as you're pushing the lower unit into place. Real hard to get things lined up without this tube. Many times it'll rattle upwards and stay on the copper supply tube when you pull the lower unit. It's just a slip fit into the pump and seats on top of the rubber water tube grommet (and the grommet does all the actual sealing of the water supply tube)
Another pesky, irritating thing to happen is when the shift shaft splines don't perfectly line up with the shift rod. Usually because there's a slight amount of pre-load on the shifter cable. So, maybe you end up a half-tooth off between the shift rod and the shift shaft. Makes it real hard to get things back together!
In that case, about the only solution is to disconnect the shift cable from the motor's shifter arm and manually move the shifter arm to proper alignment.
The above are the most common problem areas; hopefully that'll do the trick for you. Let us know if you're still having problems.
HTH & G'luck.........ed