Well, everybody's input is certainly helpful. Of course I am taking bits and pieces of it all and adapting it my situation.
Kyle, unfortunately nothing was ever lined up right since my stringer replacement. I trusted my local shop which was a mistake. I had them pull the motor before I did the stringers and drop it in and "align" it at the end. Took 2 hands to turn the prop. Its taken me until now to see the whole picture. So I am starting from scratch.
Here is my plan, and I will be doing a lot of research after this post so this may change, any input is welcome.
First step is to align strut to the log. My plan is to get a piece of pipe that fits into the log and centers the shaft as much as possible. I will find the strut position that centers it to the shaft as good as possible and put it there whether it requires grinding, spacers or fiberglass (epoxy). Now my shaft and strut are centered to the hull.
Next step is tranny install. Before this I plan on lifting the motor up by removing the two big locknuts on the jackscrews and taking a big wrench and some liquid wrench to the sliding eye bolts to make alignment much easier. The ones on the tranny were frozen in place and when I rock the motor right now it only rotates on the bushings, not the swivels like it should (and yes, the locknuts are loosened.)
Next step will be the standard motor/tranny to shaft alignment with feeler gauges at the coupler and adjusting jack screws and side to side. Now everything should be aligned to the center of the shaft log.
Am I thinking right here Kyle, TRBenj, or any other experts?