Well done and mystery solved. What made the diagnosis difficult was that the effect only took place after the engine had been idling for a long time. With an air leak you would imagine the symptoms would be the same after the engine had idled for any amount of time but here is an extreme possibility: As the manifold studs were heated they expanded and became longer thus increasing any air gap....more likely is that the engine and carb warms up and the extra weak mixture just tips over the limit for the engine to run cleanly...
Les