Sounds serious Doc...you may want to get the engine compression tested ...one scenario would be a cracked or warped head or maybe a blown gasket caused by overheating which would result in loss of power. If the spark plugs are ok testing the motor would be my next step
cheers & good luck
anyone else have issues with the alternator rotor destroying itself? I believe Yamaha have redesigned the rotor but want to charge megabucks for replacement