Sounds like an alignment problem or old hard motor mounts?. Did you have the alignment done with the boat in the water or on the hard? How many hours on the motor? Have you checked valve lash after break in? The flexible coupling sounds like a band aid cover up of some other problem. It might not help and what about clearance issues with inserting a 1/2" thick disc in the drive train? Will it even fit?
I would say go back to whomever sold you the engine and get them to sort it out. Sounds like you have already spent a small fortune there you should be made happy.
Thanks for your ideas Ted. The engine has about 100 hours, so it's barely broken in. The mechanic did adjust the valves, though he did it based on a clearance that differed from what Universal recommends. After consulting with Universal, I gapped the valves again myself. There's no difference in the vibration before or after either valve adjustment. I actually did go back to the mechanic to fix the problem, and they did a few things. They had originally installed new, stiff mounts on all four mount points, but they replaced the rear mounts with software ones. They also increased the height of the mount points, so the engine mounts lower on the mount post. Between the mechanic and myself, we've probably aligned the engine a half-dozen times now, all of them after the boat has been in the water for a week or more. Interestingly there is no vibration at idle when in reverse -- only in forward. It's much better than it was at first, and it's not going to rattle the boat apart. I'm just a perfectionist, and I have to think this thing can be made to run smooth. I'm also concerned that the Hurth transmission will wear a bit faster if I can't get rid of this vibration. It's no crisis -- just another of those strange boat mysteries.
) After installing the new diesel, replacing the cutlass bearing, shaft and coupling, carefully aligning everything and balancing the prop, there's still some excessive vibration in forward gear at low rpms. Question: is it worth installing a flexible shaft coupling?