I have a used mid 90's Yamaha 9.9 electric start and went through something similar. Mine had to have the head gasket replaced and a new thermostat. Now, idles down fine and runs like a champ. If you haven't tried them, I would recommend giving Sandy's boat house in Everett a call. If nothing else, you can buy the parts you need from them and try it yourself. I have also started faithfully running the bowl dry after flushing.