Typically,
The last thing you want to do is 'mill' the Intake Manifold.
Very true. If you do mill the intake to properly match the heads, the heads and intake should remain together on any engine it's put on. A milled intake can be used on a un-milled set of heads with a thicker intake gasket. The term "port matching" is the best way to align the ports if both parts are compatable. The gasket to be used for assembly can be a pattern for both the head surface and the intake ports. If you have a huge mis-match, you may have the wrong combination of heads or intake. (stock 273 intake on 340 J heads or the like.)