Claude, I found this article [
http://www.yachtsurvey.com/Alignment2.htm] by David Pascoe on shaft alignment. Frankly, I'm not sure where he comes out in the end on the process of alignment as much as urging that motor mounts and struts are adequate. He suggests that shaft alignment cannot be done on the hard because of hull flex. Is there a good how-to on shaft alignment?
Wufibugs, my suggestion of using the feeler gauge before re-tightening was just for him to make sure of the alignment while he is there. I am familiar with Pascoe's article and he makes a lot of good points. And he is right that motor mounts, struts and cutlass bearing need to be adequate and that the shaft needs to be centered in the shaft log. So if the mounts are worn out you will not be able to ever align properly.
My shaft is only 54" long and 1" o.d. The engine is on good adjustable rubber mounts, the shaft goes through a rubber tube and the cutlass bearing is also rubber. My 1st point here is that with as short a shaft as most of us have, if it is straight and the mounts are adjusted properly the whipping will be minimized. Might not be the case with long shafts that need support in more areas along the lenght.
While I also agree with him that a boat flexes in the water, my 2nd point would be that even if you align such a short shaft (I really mean align engine/shaft/prop) on the hard, you would need to have a tremendous amount of flexing once in the water for it to get so much out of alignment as to create a major problem. You might need to fine tune your alignment once in the water but I have always done it on the hard and never have had any problems.
Back in 2011 I came across an article by Perry Munson in Cruising World that described pretty well how I do it:
http://www.cruisingworld.com/prop-shaft-alignment.