The weakest points on these engines are the aluminum bits. Intakes can be surfaced on a smooth shop-floor by doing figure-eights with it until the mating surface is even. Just apply even pressure to the manifold whilst performing the old-school surfacing.

The head obviously requires machining if it's warped. I'd make double sure that head is flat.

Could be a lot of things, but on older iron/aluminum head engines 99/100 times it's the head.