looking forward to some answers for this problem seb as i just replaced my yam 60 with a second hand suzuki 80 and on the first trip was wondering why the motor wasn't as smooth as the yamaha and also seemed to have a bit of a howl to it as well as vibration ,the motor only has 12 hrs on it and like you was looking for the cause in the boat .
a transom plate was added whereas the yamaha was bolted direct to the transom but thats the only change.