Some tips from someone who's done it
First, if you don't have a flexible flange coupling, they are cheap and fairly easy to install. They can take up a little slack in a less than perfect alignment. Ok, now the process. Assuming that your shaft is in and your cutless bearing in good condition and your packing box tight and your shaft centered well in the thru hull, your shaft should pretty well be "fixed" into proper position. The trick then lies in motor mount adjustment. Back off your flange mounting bolts enough to creat a very small gap between flange mating surfaces. Your shoud be able to take a feeler gauge and check how "tight" it is at 12:00, 3:00, 6:00 and 9:00 postitions. you will undoubtedly feel that one or more of the positions are less tight. Say for instance that 12:00 is very tight and 6:00 is sloppy. That means your engine motor mounts need to be adjusted to make this even. In this case, you would need to drop the forward most mounts and/or raise the aft most mounts. Draw a stick drawing picture of shaft, flanges, motor and mounts to help visualize.
