First of all, if you take a stock factory exhaust manifold and match it to the head, you will be shocked at how far it can be off......1/8" is not uncommon. Some exhausts are made
bigger all around the port on purpose so there is a drop off going into the exhaust.

Headers are'nt much better; I've had to move the header bolt holes by almost 1/4" on some header models.....if I didnt, the flow would be terrible at the junction.

The best way to start the process is to find or make a gasket that matches your head....check both heads to see if they are the same. Take that new gasket/template and put it on your exhaust and see where you fall......then, make your new flanges from your template so they fit.....

What you are describing as to your fabrication of headers is essentially what the header guys do.