if they are made in the prosses that you describe, than any aftermarket header that you buy will not fit on any head, because it is not "in a terribly precise location".

The factories MUST have some talerance for the casting.

Well my plan is to make the flange, then make tools (inside and outside die/madrel) to flare the pipe to a more oval shape. and directly match the port size. (or bigger).
The pipe will then slide into the flang then be tig welded on the inside, (head side).
Any comments?