Gasket matching vs. port matching.

The gasket port sizes are sometimes oversize as you note, and so are the mounting bolt holes. Also, what if you wish to open the port size beyond gasket size? The answer is a transfer plate. Start with a sheet of metal approximately gasket thickness, drill for bolt holes and install between the head and intake. Now, drill a pair of .125 holes trough the intake flange and plate into the cylinder heads. These will serve as locating pin holes. Remove intake and grind port openings in plate perfectly flush with ports in head, transfer plate to intake manifold and use as template for grinding intake ports. Modify gasket as necessary. Now you know that with the engine assembled the ports will in fact line up.