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When playing with engine alignment you have to look at the entire system; engine, coupling, shaft, log, cutless, mounts. You dropped the FRONT of the engine to raise the shaft. Doing this made the REAR engine mounts a PIVOT point. This lifted the coupling, also lifting the entire shaft along it's length. In theory it would have the shaft pressing UP at the cutless. At best this is not a good situation because that stress is located at the output shaft and coupling. Simply put, you have caused a gap at the TOP of the coupling where the two coupling faces meet.To raise the shaft you must raise the entire engine, turning up the nuts on all four mounts. This will keep the trans output shaft and prop shaft in a perfect straight line, which is what you are attempting to do. As mentioned elsewhere you do essentialy the same for side to side movement except this is done by swinging the mounts on their slots. Keep in mind you want to keep the load the same on all four mounts. Remember, the engine and shaft as a unit must line up through the cutless and log.To accomplish this correctly you must remove all four coupling bolts. The shaft and it's coupling face are now free to move about. You need to keep them lightly in contact whole you use a feeler around the circumference. Push the feeler in to the joint as you squeeze together. Anything under .003" (three thousandths of an inch)is OK. To be certain, shake the engine on it's mounts and measure again, and again. When you get no change you're good. A flex coupling here is good because it makes the alignment of the coupling faces a lot less critical and absorbs a lot of vibration. To really do this right you would align the STRUT and cutless to the log, and there after the engine/shaft unit to them. The strut on my 1983 33 was off a good amount, which I had the opportunity to correct when I replaced the strut. But that's a whole different post which I think you'll be able to find in the archives.A side note here. Do not lean on the engine as you check the coupling gap with the feeler. Your weight will move the engine on it's mounts obscuring the true measurement. Do not ask how I learned this.