Sounds like those mounts need to be replaced. Don't know why the boat shouldn't remain in the water--and as someone else said, that's where you're going to need to do the realignment. We replaced the two forward mounts on our 2GM20 with the boat in the water--used a screw-type car jack to lift the engine just enough to slide new mounts under--engine detached from the shaft, of course.
2000 Beneteau 331
1987 Pearson 28-2
Northern Chesapeake Bay
Ambition is a poor excuse for not having enough sense to be lazy ~ Steven Wright