Have you pulled the cover off and felt each head to see if they are the same or different?
Had issues with one head on one 115 Evinrude motor (not etec so not sure if the thermostat set up has been changed) and it was to do with the thermostat housing.
I'd check temps on the heads first to see if all the same at your different speeds and then work from there if it was me.
Also whats the history with the water pump impeller? Motor hasn't been run out of the water has it?
Also the water intakes are fully clear ?
Cheers
Chimo