For your consideration, splines on drive insert into the splines on the coupler. Spline grease is used to take up the void, most use regular grease.
1-So consider this , if the splines on the drive still good ? If yes then there must be another reason.
2- Alignment or water entering the splines. I would have bet that you would have already posted that the motor was submerged past the coupler.
Troubleshoot have someone else drive the boat. You watch the back mounts and front mount as you hit waves slow and speed up.
I have to say this i never have seen a warped flywheel, i seen em rusted, no teeth abused like you never seen but warped ?
Maybe the guy doing the alignment doesn't know how ? What do you think the guy doing it knows how ?