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Mike,
Haven't read the Nor East post but part of my job is aligning pumps to motors and such.
Boy last year must have been a bit rough if off by 3/16"
This is critical.
You would want the shaft coupling to gearbox coupling within 2-3 thousanths, angular and axial. In reality on small boats you can only do this with a straight edge and feeler gauge so it never is as accurate as a rim and face dial or double dial or laser alignment so if you can get it less than 5 thou your doing good.
Final alignment you want to do in the water. All boats flex, not just old wooden boats.
Now you say this bad engine the shaft is tight now. Uncoupled to the motor the shaft will not turn easily? How many struts do you have? If the shaft is tight just going thru one and/or 2 struts and the stuffing box than that issue has to be dealt with first. This will just wear your new cutlass out fast. So yes you may have to remove the strut and shim it to the hull and let it find its home as to not bind.
When that is done. Alinging motors to shafts if they are out allot you may run out of adjustment on the mounts, may have to relocate mounts and shift the engine. You want to deal with the angular alignment first and then do the axial. On nice mounts on bigger engines you have jack screws which make things easy. You probably have this on your mounts for angular adjustments, many times and industrial situations angle iron and bolts are welded to do this task for the axial alignment. In your situation a wooden block and 10 pound hammer and crow bar for shifting the engine may have to do. Again, reality in small boats to roomy plant installations.
If I were home I'd take a look at it for you but am not now. Good Luck.
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