Last year I had a coupler go bad on my 283 checkmate convincor. It did not spin the coupler but instead sheared the teeth on the aluminum sleeve may have hit a log and binded it when taking off not sure. Anyway boat is in great shape and has fixed motor mounts in front/back and alignment tool seems to go in as should. My question is does alignment ever really get off on a application like this and if so how do you go about fixing it. I just don't want to get stranded on the river any advice or thoughts would be appreciated.

The splines get bad from a lack of grease.
Alignment can change very slightly over time. It can be adjusted by redrilling the mounts.