The best way to port a set of heads is start with a 3 angle valve job with a deep throat cut. Just a hour of blending in a 3 angle valve job will flow more air than 5 hours of smoothing and polishing the ports. An un-blended 3 angle valve job will flow about 5% more than a stock head without one. That could be 20 Hp on a 400HP car. Not bad for $100-150.
From there, you want a smooth transition from the cast surfaces into the machined areas. A good short side radius and make sure the walls blend smoothly into the throat cut. Smooth and reduce the valve guides so the air will flow around to the back side of the intake valve. Make the exhaust guides as small as you can, with whats left providing a smooth channel for air to go around the valve stem. Cylindrical shapes have 10 times the aerodynamic drag of an airfoil shape with the same cross-sectional area. Using the guides (both intake and exhaust) as a fairing will increase the airflow velocity by making the stem shape more of an airfoil and less of a cylinder.
Avoid blending on the port floor out from the short side radius. The higher the ports the more air they will flow. Lowering on the port floors can actually reduce airflow through the valve throat area. Ideally, the intake port floor should be raised a quarter inch or so, but adding material is hard to do with a die grinder. Smooth it and remove large casting flash, but take a minimum of material off. Instead, make sure the roof of the port is smooth and if you are going to gasket match take the top of each port to gasket size (leave the bottom alone).
Smooth and radius the "pushrod pinch" on the intake port, but don't remove too much material or you will ruin the head.
Have the stock valves "back cut" while the 3 angle valve job is being preformed. This will remove the ridge at the valve seat and the valve will flow more air at low lifts. Many performance machine shops will do this very cheaply and the result will flow comparable to aftermarket stainless valves (that are manufactured without the ridge) especailly at the low lifts our cams run.
The best tool to port with is doublecut carbide burrs. they are relatively expensive, but can last a very long time. They will cut through cast iron like butter, so you have to use caution. After everything has been roughed to shape, sandpape rolls do a good job smoothing.