@swbca Back to your priority question of fixing the boat vibration...it sounds like you know all the checks to be made. Checking the shaft alignment at the coupler is fairly simple. Get some feeler gauges, remove the coupler bolts and start with that. Examine your strut for any damage if alignment is way off. Be sure the strut is firmly mounted to the hull, most likely it is. And, being an older boat, you may need a new strut bearing installed if you can feel much play of the shaft in the strut; there should be a little play, very little. Inspect for any prop damage, if in doubt, have a prop shop check it for balance. Check all your engine mounts to be sure they are secure to the engine, and to the boat structure. Lastly, you may need to pull your shaft and check that it is not bent. Even a slight bend can generate a good bit of vibration.
During 4 decades of inboard boat ownership, if I feel vibration in the pylon while underway, that's my cue to check the items above. Alignment is what resolved most issues.
Fix the the vibration before it causes other issues.
Good luck, keep us posted.