I finally got back to work on my baby over the weekend. I aligned the motor to the prop shaft within about .002" but the motor is now "angled" toward the port side. The front starboard trunion is over-extended by about 1/2".
When I did the alignment I inserted a rubber bushing in the shaft log to keep the shaft centered at the "top" of the log, but I wonder if the shaft is not centered at the "bottom" of the log under the boat, suggesting a bent strut.
Hmm . . . or am I over-analyzing things?