[Chuck Sea/Tac]

That stud hole may have rusted through into the water jacket, so you need a thread sealer like permatex. There’s not much you can do to the deck without a disassembly and machine shop. Usually the deck gets off around the corners in the water jacket area, but usually seals fine. .002” is the acceptable unevenness allowed. You can take almost all the combustion chamber off on the head. The problem is, has the block been decked? I’d worry about the pistons hitting the head, before the valves. You can do a test fit with a used gasket and clay or tinfoil balls to find any interference.