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When I replaced our engine mounts, I had to get longer lag screws to tighten the mounts to the bed since the original screws no longer had sufficient bite into the wood. If these screws are loose the engine will not stay aligned. A quick alignment check: With the transmission in neutral (and not running), you should be able to rotate the prop shaft by hand, by holding onto the coupling. If not, something is wrong....misaligned, packing gland too tight, etc. If you have a folding or feathering prop that is not operating correctly it might cause a vibration that would show up when the engine is in gear, or a bent blade on a fixed prop. Other possibilities are a worn out cutlass bearing or a broken or loose strut.

Also take a look at the engine mounts and compare the spacing between the top inverted U bracket at the front and rear of each mount and the base plate. According to the Yanmar installation manual, a correctly installed engine should have approximately equal space on both ends of the upper U bracket. If the U bracket is in hard contact with the base plate then there is no vibration isolation from the mount and it would be difficult to align. On my boat, even with all new engine mounts, one aft mount nearly touches the base plate. According to my measurements, considering the down angle transmission and shaft angle, I think the engine beds are at the wrong angle. I considered shimming the rear mounts, but that would use up too much adjustment range for alignment, so we've just left it alone.