I had a Jenneau 54 DS come apart on me in the middle of the pacific once. This is unrelated to your vibration (I'm assuming), but maybe worth a look while you're in this
project.
What happened was that the stringers that comprise the "box" that is the foundation for the
steering quandrant bracket or "base" - they are not reinforced with any
hardware at their joints...they just glassed these together. It's a design flaw. Once you get into some big waves the flexing of the
boat literally broke the seams/joints loose, then causing play in the shaft and the
boat started taking on
water. We had to turn around 600 miles
offshore and limp home after jury
rigging some line and a twister to hold the quadrant down.
Jenneau got involved but didn't pay for any of the
refit, even though they admitted it was a faulty design on their part.
So, bring it up to the yard and have a look in there while you have it apart, if you see the same construction fab some kind of reinforcement for this boat.