I remember trying to help align an engine in Badger's lazarette, in a Falkland Islands' winter, approximately 100 miles from anywhere you could by anything. We had bought one of those thickness gauge thingies and I was reliably informed that the tolerances had to be +/- this much. Are you kidding? Shims were cut from beer cans that were fortunately to hand. Beer-can shim cut hand, too, come to think of it. Lots of blood and bad language. An additional quirk was that the engine was on quite a steep slope and heavy. Not that stable and difficult to support (oh yes, it was off centre at one side of the boat). We got there in the end but I remember thinking 2 things: (1) I don't want to do that again. Ever. (2) Now I know why they invented sail drives.
So I feel for you in your plight, Gary and hope that having got things lined up nicely for the shaft, all the rest goes smoothly.