Hanley, thank you for the motor mount oil tip. I finished up the shaft log repair this weekend and will start lining up the new shaft this week. From what I've been reading I will need to recheck the alignment once in the water for a few days.
Sounds like you've got it right. Before you get started it's a good idea to loosen the nuts on the motor mount studs and apply some oil so they move easily when you want to make adjustments.