Good luck with the dial indicator, unless you have the shaft on a lathe. If you have a misalignment at the hub, and you rotate the shaft, it can potentially give you a false reading. You'll get data, but whether or not its really worth anything remains to be seen. Naturally, if you have a badly bent shaft and it's wobbling in the center, and good at the hub and strut bearing, that will show.
Props can be pulled and checked, not a bad idea if you have vibration. Bearings can also be checked pretty well with a visual. I am surprised that some bearing manufacturers have a tight fit when new and others don't. Just depends on the brand you select.
Here is a nice article by David Pascoe on alignment, and it is well worth reading!
http://www.yachtsurvey.com/alignment.htm
Morse
Johnson Duramax Cutless
Prop and strut bearing puller
http://www.mindermanmarine.com/prop_puller.htm
Everyone ought to have two or three of these things in their tool chest, lol.
http://www.strutpro.com/
regards,
Paul