We used to start cars with no transmission in them. I don't see a problem with that. The two motor mounts and, usually, a bottle jack under the back of the engine was all we ever used. Of course, be extremely careful when you start peeking at the moving parts.
Regarding starter motor measurements, the only thing I have is the Ford Shop Manuals that show correct, and incorrect, teeth markings between the starter motor and the flywheel. Unfortunately (or, fortunately, depending on how you look at it), I have never had a starter motor alignment issue on any car, ever. Datsuns to Fords, they've always just lined right up and I never had a problem.
Now, when it comes to aligning your bellhousing, I think you have to treat it as though it is completely unknown. Install it as if it were a permanent, and then put your dial gauge on it and see what the run out is. Usually, when it's done properly once, you don't have to screw with it again. But in your case, you have to double check everything with a jaundice eye as to how it was originally set up. (medical joke there, get it?)