I found that the valve areas needed the most work. Casting lines and imperfections need attention. Also, the valve seats can be ported out to match the port better.
A non-ferrus cutting bit works really well for rough cutting the port, while leaving a little material removal for when you're sanding/polishing the port. I used sanding drums to clean it up smooth (I forget what grits, but a search on the old forums would tell you what you need to know) and cross buffs to polish everything up well.
Generally, I would gasket match the intake side, and port match the exhast side to the headers you're using.
The old forum has tons of info in it. I know I personally gave out gobs of info on what I did, and I know others did too. Bench flow #'s and real world data.