Did you check the incomming water strainer. There should be one in line. They sometimes get stuff in there that will restrict the incomming flow somewhat, but your exhaust output is still decent because the water muffler fills with water. Also check the pickup on the bottom of the boat and make sure there is no damage or blockage there.
Also check the impellar housing in/out ports and flush the entire cooling system with a water hose. If an impellar came apart at some point, it can get stuck in the passages and restrict flow.
If possible run the genny on a hose at the house or marina. You can go to home depot and get a standard home washing machine rubber water supply hose, cut off one end. You will find it will slide into the water supply line of the genny perfectly. Use a hose clamp on the genny hose to tighen up the fit.
Pull all the lines and flush them forward and backwards, then run it on the hose. If it still runs hot replace the temp sensor.
If this doesnt work, call Kohler.