Flywheel housing question

[Towd56]

I've read just about every post regarding how to align the housing . I know you should have no more than .006 between the 12, 3, and 9 o'clock positions.

Here is my million dollar question:

Once you bolt the housing to the trans- aren't all these tolerances going to change? Won't bolting the housing to the tranny "straighten" any variance you have?

I'm currently about .025 out between the three positions. I'm trying to wrap my head around this before I go cutting the housing.