There doesn't seem to be sufficient clearance to soundproof these surfaces. The impact of vibration seems to be greater than that of direct engine noise. The vibration generates sympathetic vibrations in lockers, drawers, the stove, hasps, fire extinguisher brackets, etc. I've wrapped the fire extinguisher bracket and sail locker hasps with self-bonding sail tape and installed pads on the companionway ladder feet and on the head and aft cabin door frames to prevent vibration. No shaft or prop problems.
Shaft is aligned well.
Compared to many boats mine is smooth and quiet. Unfortunately, I've seen just how smooth and quiet a sailboat can be under power and I liked it. The engine compartment is about as insulated as you can get it given the room and clearances. Most of my complaints would go away if could just stop the harmonic vibrations the engine sets up at several rpm ranges. These are not shaft alignment vibrations as they occur in the same ranges whether in gear or sitting in the slip in neutral and the shaft is aligned per specs.