Have any of you heared of transfer screws. Transfer screws are hardened set screws with a point. Thread them into the tapped hole with a special tool place the header flange stock over the bolt pattern. Hit the flange with a hammer. You now have the desired bolt pattern. Drill a starter hole for the port then die grind to to match the cylinder head. The problem with this type of precision is that the dimensions change with temperature. Headers can get cherry red and the cylinder head doesen't get nearly that hot. The cylinder head has greater mass than the headers so they change temperature at different rates. The holes in the exhaust manifold or header flange are large to allow for this. If you are in school and have access to fancy tools ask your instructor about an inspection machine or ask how to take measurements using your milling machine.