Re: Transmission output flange fell off Yanmar 2QM15 - Theories re: why?
It is possible that the vibration that you now feel is from the new flange, and the old transmission shaft not mating perfectly. The new flange surface should be exactly perpendicular to the axis of rotation of the flange. This isn't likely to happen unless you can get the transmission and the flange to a good machine shop.
However, you might try the following simple fix to lessen the issue; remove the bolts holding the prop shaft coupling to the transmission output flange. Align the holes so that the next hole on the propeller shaft aligns with any given hole on the transmission output shaft (move it one hole). Put everything back together, and try it out.
If the characteristic of the vibration changes, you confirmed my theory. If it changes for the better, keep it there. If it changes for the worse, try aligning a different set of holes.
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USCG Licensed OUPV Captain, ASA 101/103/104/105/106/118 Certified Instructor - Also certified in Recreational Marine Electrical Systems