360 Head Question

The heads are decent, they'll work fine for a mild build. If you're rebuilding them, bigger valves aren't a bad thing (2.02/1.60). If not, they'll still be fine.

The holes under the exhaust ports are smog ports, as aarcuda said just tap them 1/4-20 and put in set screws. Only tap them as deep as you need to go to get the set screw in, that way you don't have to worry about the set screw ending up somewhere it shouldn't be. You can weld them up too if you're so inclined, just make sure they're smooth when your done so your headers seal.