Yanmar super vibration

Have you checked the valves? If diesels miss, they produce some disturbing noises. If one valve is hanging or needs adjustment, it could produce this condition under load. You are absolutely right to avoid an expensive fishing expedition! Take it piece by by piece to eliminate everything until you are certain what the problem is. Compression test? Maybe try releasing compression when this occurs. If slowly releasing compression on one cylinder has no effect, it might narrow the problem down to either a bad injector or a leaky valve. Have you checked for obvious air leaks in the fuel lines? Maybe give all the connections a tweak, especially those injector banjo fittings which tighten down on the copper washers (use a torque wrench). Do you have a shop manual?

Brent Swain said:

Those super soft , nothing but rubber connecting the engine to the boat, Yanmar mounts are dangerous. A boat was sunk off Queensland last year, when the engine came loose and punched a hole in the hull. Perko makes harder mounts with metal holding things together, if the rubber gives out.

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Don't want to throw this thread off the tracks but you are right about the danger of the rubber mounts. That said, to avoid the "flying large projectile" problem inherent in these mounts, cable or Amsteel should be threaded through the upper and lower components so the engine can't go far. It's a good use for four soft shackles.