So I picked up the boat today after the shaft was straightened and reinstalled. I was underway and once we got going I opened the hatch to the engine room. I took a peek at the starboard engine and it was no longer shaking. All was well. Phew. I looked over at the port engine, and to my horror it was moving all over the place. If you recall, my port engine was fine, but the starboard engine was vibrating due to the bent shaft.
Apparently, when the boat yard put the boat back in the water and adjusted the alignment on the starboard engine after the shaft reinstallation, they decided to check the port engine alignment too. They said it was way out of alignment and they said they adjusted it. After I returned to the boat yard to tell them that the port engine was shaking, they were a bit bewildered. Their theory was that the port shaft may also be bent, and now that they fixed the alignment, it's causing the engine too vibrate at low rpm. It also looked like it was leaking a bit of water through the shaft seal, which it had never done. I said it hadn't done either before. They said that before when the alignment was off, the shaft was probably moving toward the prop, but now that it is aligned, it is moving closer to the engine.
Does this sound logical?
It's a major bummer.
Note that whereas the starboard engine vibrated more in the midrange, this engine movement on the port side goes away around 1,400 rom but is far worse than the other engine was in terms of movement under 1,000 rpm.