Kyle, there are 3 problems, not 2.
1. Transmission rebuild
2. Strut to log alignment
3. Powertrain to shaft alignment
Agreed that working on #3 without verifying #1 is fixed is probably a waste, as you need to perform a powertrain alignment every time things come apart. Working on #2 is completely independent of the other things, and certainly wont need to be redone every time the tranny comes out. The fewer things in the way, the better (so Id do it now while the tranny is out) but it can certainly be done anytime.
Scot, it sounds like youve got the basic concept down. Use the old shaft for all of your strut to log alignment checks (dry fits). Once you finalize your strut mounting scheme (shims, grinding, whatever) then go ahead and bed it down in 5200... and check the alignment again with the old shaft. The strut can move around enough in the bolt holes to cause the shaft to hit the log. I'd snug up the strut hardware, check the alignment, and adjust the strut position with a BFH if necessary (it usually is) to get it perfectly centered again.
Remember that the point youre aligning to is where the shaft spins freely in the strut. There is come clearance and squish in the shaft bushing that will allow the front end of the shaft to sag under its own weight- make sure you dont align to this point.
I would not agree that grooving in the shaft at the strut bushing to be "normal". Smooth and polished, yes. But if you can catch a groove with your finger nail, its junk.