So if I follow this, port engine had no vibration when you started down this path.
As part of the stbd work, they checked the port alignment and found it to be way out. They realigned it, and now it vibrates badly.
All this suggest that for whatever reason, their assessment that the port side was way out of alignment was incorrect, and that their realignment induced the vibration. Not sure why they found it to be so far out, but this seems to be the most likely thing.
I think Ski is right that there is no need to panic. Unless they somehow bent the shaft handling the boat, this is probably just a simple mistake that was made. I suspect that a re-check will show an engine way out alignment, and re-aligning again will restore it to it's previous performance.
Just spoke to the yard. They spent another 6 hours (not billed) to remedy the issue. They said it is better, but I don't think it has been eliminated. In fact, my strong assumption is that when I see it, it will probably still be serious enough that I'll want to continue to address it. Just a hunch.
I do strongly believe that they have a capable technician working on this. It is their most senior technician.
They took the boat out of the water again and checked the prop. Prop was okay. They checked the shaft. No runout. Shaft was fine. They checked the cutlass bearing. It was fine.
They put it back in the water and disconnected the coupling completely and it was supposedly really easy to move the engine around as the mounts are very soft.
So they tried again to align it, and whereas last time they aligned it and it was off by 6 thousandths, it is now 3 thousandths. Yet there is still vibration. Actually, more of a shake like before. But they said it is much better. We'll see if it is truly "much better" when I see it for myself.
They also called the local Volvo shop (Helmut's Marine) and conferred with them.
I also called the guy who serviced my Volvos about a month ago. The one thing he could think of is that he said he's seen a few cases of where the facing of the coupler is off, in which case it wouldn't matter how much time they spent trying to align it, as it would still be off. He said he's seen instances where it is fine, but if you move it even one bolt hole over on the coupler, it can then be off. I may have lost a bit of detail in my translation, but hopefully you get the gist of it.
Thanks,
Mike