Look to me like the EGR feed holes. Looking at the EGR pad (never really looked at Chev EGR setups closely) is the "feed" portion (what feeds those holes) where the EGR mounts seperated by a cast aluminum "wall"?
Basically, you need to make sure that if you run a blockoff plate, the EGR feed passageway (the center crossover in the intake) is no longer allowing that crossover to feed those holes.
Buddy put a blockoff plate on his chev motor at one time, ran like crud. Put an EGR back on, but didn't hook it up, problem solved.