The ports in the head are an exhaust crossover to provide some heat to the carb and operate the choke in cold weather driving. The passenger side stock exhaust manifold had a butterfly valve in it that would be closed when cold thereby sending the exhaust over to the other side through a port in the intake.
Really unnecessary unless you live where it snows. Unfortunately it stays hot after the choke has done its job and will rob you of HP. It is common practice to just plug the openings when replacing the intake gaskets.