Vtotten:
Glad that you have discovered the possible (probable) cause of the sudden vibration. Something coming loose at the engine/transmission-to-shaft coupling did flash through my mind when you first posted -- particularly since you had an after-market re-powering not too long ago. But prior to your more detailed look-see, there were just too many possible causes to conjecture about. It's possible that your installer might not have torqued the coupling bolts well enough. Or in any case many new installs require inspections and re-torque of various fasteners (like engine head bolts, car wheels and suspension items, etc) that might get loose after the initial "break-in" period of service. If your new engine came with a manual, you might check what other special "new engine" service items there were. And if not done, follow-up? On the positive side about your coupling, the engine shaft interface is notorious as a site for ugly rusting. Not your case. I've seen pictures of older boats where there is no way the coupling bolts can come loose -- rusted in place instead!