Thinking about your problem If your sure you have WATER FLOW then i would check the thermostat as i just changed one that was stuck CLOSED
It allowed full water flow through the bypass and into the exhaust manifold BUT NO flow through the block which is were the temperature sender is so it got HOT
I cant really see how exhaust could flow through a water lift muffler and NOT water so you need to take a picture as there again no standard install
And one final thought the exaust manifold is the final place ALL water has to flow through and it could be blocked