Following is an excerpt from the Guestlog section of Don Moyer's website:

"I prepared the following instructions after going through the rigors of aligning my own prop shaft last winter. Hopefully, they will help you. They were prepared from the perspective of having an engine already installed, so you may have to pick and choose which of the steps apply:

1) Disconnect the exhaust pipe and anything else that would inhibit the free sideways and vertical movement of the engine.

2) Check to be sure that your stuffing box hose has not hardened over years and displaced your prop shaft away from the centerline of your shaft log and cutlass bearing. In my case, the center line of my prop shaft had moved so far that I had literally run out of adjustment on my mounts. In fact, my oil pan was practically hitting the side of the engine room before I finally figured out that my decades-old stuffing box hose had moved so far that it was impossible to catch up with it with my adjustments. I replaced the stuffing box with a PSSA mechanical dripless seal from West Marine and started over again with my adjustments.

3) After assuring that you have control of your prop shaft, and that you know where its center point is with respect to the cutlass bearing and shaft log, pull the shaft against the output coupling of the engine and be sure that the prop shaft coupling and engine coupling line up with each other. In most cases, the OD's of the couplings are the same, so you can simply check that their OD's line up with each other. If the couplings do not meet each other, your first step is to raise or lower the engine until they do.

4) After assuring that the center line of the engine coupling and the center line of the prop shaft are aiming at the same point in space, you are ready to check the actual alignment of the engine and prop shaft. You do this by inserting a feeler gauge between the upper, lower, left, and right quadrants of the couplings.

I find it easiest to deal with the lateral alignment first. If you have a rail mounted engine, you may be able to rely on your original left/right alignment, but if you have adjustable mounts, you will probably have to recheck their location. In either case, if the feeler gauge (I settled on a .003" gauge) shows that there is more space at the three o'clock location than the nine o'clock position, you'll have to tug and pull on the engine until you measure the same tightness of your feeler gauge on both sides.

5) After aligning the engine laterally to within a couple thousandths, do the same with the vertical alignment. If you have adjustable mounts, vertical adjustment is the easier of the two perimeters. If you have a rail mounted engine, you'll have to add and subtract shims fore and aft until you measure the same feel of the gauge at the twelve and six o'clock positions."