Good reminder on the top nuts. The yard did the alignment, so I never checked. I've never owned a diesel other than the Yanmar so I have nothing to compare it to, but it does shake at idol, especially when you replace the control cables and the idle drops down to 500rpm (fixed now to 800rpm using the idle set bolt instead of the control cable). I'll check the nuts next time I'm on the boat.On the engine vibration issue: What is your prop tip clearance from the hull? You need at least 2". Check the top nuts on the engine mounts--Yanmar tries to take engine vibration into their mounts (rather than into the boat--that is why Yanmar's shake more when idling) and if they are not tight they can quickly work loose.. I have forgotten to snug them. The engine may settle on the mounts a bit after reinstallaton and require adjustment. Just brainstorming here.
I did have the shaft cut down to reduce the shaft between the end of the strut and the propeller. If I remember correctly, the minimum clearance is 10% of the prop diameter. I have a 14" Campbel Sailor, so around1.5" should be good. I think I'm at 2-3". Here's a pic right before we put it in the water