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IIRC, the amount to mill the intake flange vs. the cyl head deck surface is close to 1:1. That's what I've used, wiht no fitment issues after. The problem is, you are milling the flange the valve cover seals on too. So there is a finite amount you can remove before you either have very little sealing surface left, or the bolt holes get in the way. The max I'll mill off is .030" from the intake flange. You can mill about .020 off the deck surface without seriously compromising the bolt hole alingment, but you will compromise the port alignment, which for some (me included) is a is a big deal. I'd rather mill an intake to fit a set of heads, and get the power the engine can really make running the right intake the first time, then compromise the output on the premise of "I'm using the wrong intake and need to swap it..." Also, the valve covers may need to be trimmed to fit the heads and clear the intake runners when you mill a lot.