We had to raise one of our 135 Lemans 2 inches, to change to a twin disc trans. In doing so, of course we had to align the shafts. One of the biggest challenges, was just lifting the engines. We had heard of horror stories of people jacking under the oil pan, big no,no. We used a cut down 4x4 straddled over our water tanks, with a chain hoist. Some use bottle jacks. Access, to the outboard mounts, can also be a pain in the neck. The alignment, is easy, of course, once we had a system. The ideal gap between the face of the couplings, is .003.
Which is checked 12, 6, 3, 9 o'clock positions on the face of the coupling. The adjustment is done by adjusting the height on each motor mount, a quarter of a turn at a time. For example, raise the left front mount, and hence, the opposite aft, will close in space. My wife devised a system after a few days of too much wine, from the agg factor. She made a pie chart, with 12, 6, 3 and9, and after she and I would adjust one mount, a quarter of a turn, check the flange for any change in .000. Just Remember this is not rocket science. After this drama, we aligned both our engines, whenever the boat, was refloated. Zero vibration, and no need for a damper
You can do this, my wife is a pharmacist, and I am a car guy since a kid.
Feel free to ask away, we have done it many times over the yesrs..