Doubtful it's an issue with the Air Gap design, many people run them without this issue. Which is not to say your specific manifold doesn't have an issue.
Years ago I ran into an engine that had the two outer plugs on one side and the two inner plugs on the other side all carbon fouled. All four plugs were fed by the same half of a QJ. The carb was in need of a rebuild.
Look at commonality issues is my suggestion. You realize the three cylinders you are having issues with follow each other in the firing order? Did you look at that?
