Sounds like it would be a good idea to get the dial indicator set up to indicate on the transmission mounting bore on the bell housing.

The factory dialed in the bell with the particular block... mixing and matching parts later can get you off quite a bit. Worst are some steel bells.

I do it by mounting strip steel on the flywheel or crank flange and bend cold to get the dial indicator in the right spot. Offset dowels as needed to get it dialed in. <.003" preferred, .005" max runnout.