Hi,
This sounds like a heat build-up problem. And after everything you have done its probably not going to be an easy to find one either.
Like old Chevys, here is a couple of things I would look at first. Is the petrol pipe routed too close to the the engine and its picking up heat? Does the carb have a very good gasket at the head mount, and is it tight? (heat opening a gap where they meet after a short run).
Another thing I would try before I tore everything apart again, is build some type of quick heat shield, (like a piece of tin) and slide/strap this between the carb and the head- try to protect as much of the fuel system as possible (underside of the tank and fuel pipes too). Then go for a ride and see if it makes any diff at all. This will eliminate an awful lot of things and its quick to do.
I could be way off base here, but I have seen this twice on different vehicles now. Its not that the engine is overheating at all, its just something very minor that heat effects.
Lee