the sound i had on my bike i thought was coming from the gear box too! But i found out it was a worn rotor and the antirattle cage inside the caliper was bent..i straightended it out have a new rotor on order and replaced the pads..noise is gone. I also had a clicking sound i thought was coming from the engine,but i found out it was the fuel pump..it was on it last legs...it was also making it hard to start it up in the mornings! Cycling the kill switch on and off between starts cycles the pump if itsa little shaky!