The following short video clip is of a drive line noise I am trying to resolve. (see Hurth bent fingers thread for background).  I am standing in the reat lazerette.  The frequency of the noise matches the RPM of the prop shaft.  The noise presents in gear or while in neutral and free spinning at 6.5 kts until the prop stops spinning on its own.  The noise manifested after the prop shaft and cutlass bearing were replaced and PSS installed.  My boat had a short haul a few days ago in an attempt to resolve.  The propeller, zinc, cutlass bearing  checked out fine.  Thinking the cutlass bearing was checked for a set screw to prevent it from spinning? No runout gage was used to check for a bent prop shaft.  It was observed that the prop shaft favored the port side of the fiberglass log.  Everything else appeared fine.  The engine is going to be realigned (for the 3rd time) this week.

http://youtu.be/N_qJ4RbwF4Y
I was present when a shop removed the original bronze drive shaft (too much wear to accommodate a PSS).  The prop shaft appeared to require a good amount of force to bend it around the rudder.  I believe the cutlass bearing was removed from the strut afterwards, but it could have been removed before.  I was not present for the reinstall with a new SS prop shaft an cutlass bearing, but the rudder was not removed.
Is removing and reinstalling the prop shaft with the rudder installed standard procedure?  It is possible to bend, perhaps dislodge, or damage the strut?
Could the new SS prop shaft be bent during the reinstall so it no longer runs true?
What could be the source of the noise and resulting vibration?
I searched for responses to these questions.  Sorry if I overlooked the answers.
I appreciated any help that can be provided.  To say I am in a pickle is an understatement....