When hooked to earmuffs an engine really isn't getting the same water flow it gets with the impeller submerged in water. I tell friends if they are going to flush with muffs to first turn on the water and squeeze the muffs against the sides of the lower unit - you can actually hear the water being forced up through the impeller and lower unit. Then, get clear of it and start it.
That engine is known for this. I'd start at the thermostats and impeller, impeller housing and the impeller plate it sits on. If the impeller housing if it isn't perfectly smooth or feels like it has groves cut in it could lower pressure - same with the plate the impeller sits on - it should be perfectly smooth with no grooves ground into it. As far as the thermostats go - put them in a pot of water on the stove and turn on the heat (can also stick a thermometer in the water while doing this) and see if they open and at what temp.
Also, what is are your idle RPM's when it is IN the water? Idle RPM should be around 750. Lower RPM than that can set off the alarm.
Lastly, google "Yamaha 225 ox66 poppet valve". That can cause these warnings and I believe there is a better made replacement valve now if necessary. Some report that just lightly stretching out that internal spring a bit and putting all back together solved the problem.
