Suggestions and comments.....
Manny
Simply align your engine as close as possible using feeler gauges. Try to be as precise as possible so that when you are using the feeler gages (doesnt matter WHAT value/thickness of gage you use) the feeler gage is retracted from the coupling, etc. joint ***with the same approximate amount of hand force***; .... this will insure that the face to face alignment of the coupler is within .001 - .002 inches. All you are doing is adjusting so that the 'faces' of the coupler are **parallel** when you assemble it back together. Dont make this a mathematical nightmare of endless calculations .... just choose 'any' feeler gage, insert it between the coupler faces, move the coupler faces together WITH the gage between, make sure that it withdraws with the ***same force*** at 4-6 places around the circumference .... USE THE FORCE, Luke!
If the prop and shaft is unbent and the blades are clean there will be no induced side forces that will make the shaft 'whip' when rotating under load. Thrust is 'axial' along the shaft and can be totally ignored if the shaft is 'beefy enough' (the shaft would have been already 'knocking and banging' if there already was a 'whip problem') ..... this all assumes that the OEM design engineer did a good job; so, there is no need to 'contemplate someone else's navel'.
If you suspect the very remote possibility that the propshaft has been bent, after you closely align and assemble the faces/coupler, etc., simply use a dial-indicator gage somewhere near the 'mid-span' of the shaft, rotate it and measure the 'run-out'. If you dont have a dial indicator, just put 'something close' to the shaft so that there is the 'teeniest' gap between the shaft and the 'something', put a strong light underneath all and simply visualize how much actual run-out there is when you turn the shaft. If 'significant' then measure the run-out by turning the shaft in ~90° increments, etc. while using feeler gages between the shaft and the 'something'.
Keep it simple; use the force, Luke.