Scottly,
Good thought, but again, not the case. I think it is just bad machining tolerances. I'm just trying to figure out if it is worth it to machine the top of the spark plug hole more to lower the spark plug into the chamber.
Here's my flow bench set up. I just set up a comparison bench. I wasn't concerned with calculating actual air flow. I found that one intake port was over 35% harder to breath through than the other three, and one of the exhaust ports was much worse. I shaped bowls over the intake valves to start with, then opened up throats/runners to match the cylinders. I could feel the difference in the port with my finger, and verified it with the flow bench. I followed advice I gleaned from here and the internet on how to shape the ports.
First pic is the box. I bought a storage container and cut a hole in the side for a shop vac hose to fit in (you can see it took a few attempts to cut a good hole):
Second pic is a plywood board with holes cut in for the cylinders to protrude through. I glued rubber mat onto the board to create a seal between the box, jugs, and board.
Third pic is the partial assembly. I put all of the dowels in place when I put the head on the jugs, but I did not use any gaskets. The weight of the head and jugs was enough to seal to the board, and my head and jugs sealed very well to each other without being bolted together.
Fourth pic is a yardstick with four clear rubber tubes.
I placed the bottom of the yardstick (the short length of rubber tubes) in a shallow bucket of water. The longer ends of the tubes were placed on the intake ports just like you would do if synchronizing the cylinders. I repeated this on the exhaust side by cutting 8" lengths off a junk header, drilliing and tapping them to take a sync nipple, bolting them to the head, and repeating like i was synching the exhaust. When flowing the intake, I installed the exhaust valves completely and installed the intake valves backwards to mimic the shaft of the valve being in the airflow. I used the same procedure for the exhaust. The spark plugs were all installed during this test.
The shop vac pulled plenty of vacuum to make the water rise up the rubber tubes. There was almost no variation in the water level since the shop vac pulled at a constant rate (not like an idling engine). Since all four cylinder were being flowed by a common plenum, I was comfortable assuming they were all experiencing the same pressure drop for comparing flow rates.
In addition to evening the individual ports, I blended the intake runners and ground down the portion of the carb sync screws that stuck into the airflow.