Re: johnson 15hp
Tempted to say its the drive shaft not coming away from the crankshaft but I dont think it would drop as much as 2" if it was that.
Sure you have fully disconnected the joint in the shift rod.
Some engines have a pin through the top of the drive shaft that has to be properly aligned but I dont think that applies, anyway i dont think that would allow it to come down by two inches.
Is it a long shaft model? IF so take the extension piece off with the gearcase and then remove that after cleaning up the drive shaft. Forcing it will result in the pump impeller pin damaging the water pump casing. The drive shaft runs in a bush in the extension and wont slide through it until cleaned up! (dont ask how I know this)