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Tubs,
I pulled the water lines off and did as you suggested. The cylinders held similar volumes of water in the water jacket. I blew air through them again. When going back and forth, one small flake came out of the cylinder that was getting hot. I may have been enough to block the outlet on my last test run. After re-assembly, the port cylinder is still warmer than the strbord cylinder by 15-20 degrees depending on where you check, but it now runs cool enough that you can hold the cylinder while running.
The only thing left to do is better seal the fuel line fiting at the carb. It has a filter screen in there. I pinched two gaskets to go above and below the screen, but I am still getting a small leak. I am afraid to tighten the large nut too tight and break something. The original gasket seemed to be similar to heavy Kraft paper. I have used the thicked grey fiber type gasket stock.
After this, it will sit until warm weather allows for a lake test.