Dan - I had the same symptoms before I cleaned out the water passages in the head. The front cylinder was pretty much scaled up, and in some spots the scale had turned to hard carbon blocking the passages. I had virtually no water flow around it before the cleaning. I'd get the high temp alarm after slowing down subsequent to running higher speeds. The reduced flow from the water pump at lower RPM wasn't enough to take care of the heat that had built up.
I know you're fresh water cooled, but consider taking off the manifold that the thermostat screws into and see if there is any obvious build-up/blockage there. You also may want to check the thermostat and make sure it opens in a cup of boiling water.
Second thing I found after I rebuilt the engine was the water pump bearing going bad and finally seized. I replaced the pump and have noticed significant improvement in the water flow out the exhaust spray. I rebuilt the old pump and include it in a bag with my "cruising spares".