There is a wonderful thread on this forum by one of the Kirkham brothers who takes you through each step of aligning a QT bellhousing with very nice pictures and explanations. There is a small bit of math involved, but not much. Basically, you just put your run-out gauge in the middle of the BH and adjust the two dowels so it's perfectly centered (that's the simple, one sentence answer
). My Lakewood took quite a while to do, and it was on an engine stand. Obviously it's harder to do when the engine is in the car. Do a quick search and you'll find the Kirkham thread. It might have been contained in the big thread on the million dollar Cobra they built for Larry E., but maybe not.