I wouldn't worry about the holes between the ports.
The airflow is not even going to notice them.
With both ports nearly the same diameter the air pressure on both sides would be equal as well.
Both primary and secondary ports dump into the same cylinder. Both ports will pull the same amount of air each time (since the engine is a fixed air pump)
The air flow is mainly down the center of the ports. The airflow directly at the walls is considerably slower. (buffer)
The engine will pull the air in from the path of least resistance. That would be the 34mm hole rather than the 3mm one (which would also have equal vacuum from the opposing port).
