I would encourage you guys not to use the offset dowel pin alignment procedure. It is imprecise, does not repeat with bell housing removal and replacement (w/o readjustment) and (as has been already been noted) changes as you tighten the bell housing attaching bolts.
About a year ago I did a write up on how to align the bellhousings to the blocks. It covered both the why and also the how to questions. If you are interested it's already on Club Cobra, click here =>
Bellhousing Alignment
The technique I describe will consistently allow you to bring the TIR to 0.001" or less.
Ed