I've read quite a few articles on the web since this thread started. The basic idea is to match head/manifold openings and smooth out the existing port, nothing more. Because the air's velocity at different rpms will effect the engines performance. Just making them bigger would most likely help the engine breath at high rpms but because of the slower velocity at low rpm you'll loose bottom end torque.
So basically you mark out where the gasket sits on the head. Grind the openings to match the gasket tappering in about 1.5". Then remove any casting lumps, bumps and shape edges and then smooth out whats left. Basically you're not looking to greatly alter the the size and shape of the port but to just fine tune it.
Then the intake is marked up similar to the head but this time you grind slightly smaller to ensure smooth flow into the head incase of any small error when re-assembling. The exhaust is made slightly larger and polished mirror smooth to help resist carbon buildup.