I have the same Yanmar in my Beneteau. I put about 50 hrs on the engine per season. The engine has about 300 hrs total on her as I write this post. During the third season the engine started to vibrate at idle so bad it would shake the whole
rig. Sounded something awful. After she gained some rpm’s she would smooth out. This puzzled me for some time. What I found was that my throttle cable had stretched and had dropped the idle speed down. Causing the engine to drop a cylinder (firing on only one.) After readjusting the cable (on the left side on the engine as you are facing it) to bring the idle speed back up, no more shaking. Let me know if it works for you, Regards Mike