If you've managed to plug the heat exchanger in your water heater, that probably speaks volumes to the amount of crud in your engine's freshwater cooling system.
I've never heard of a heat exchanger in a water heater getting plugged. I would view that as a symptom of another problem, maybe reduced performance / wear out of your freshwater engine pump.
Btw, you can probably clear the blockage by removing the coolant hoses from the water heater and back flushing the heat exchanger with domestic water pressure. The engine coolant loop has almost no pressure, so the loop bypasses or stops flowing easily.
As mentioned above, I would consider flushing your engine's coolant system before you find that a cylinder isn't getting properly cooled.
Ted