describe the beeping sound. Does it pulse, does it get louder with speed or rpm, or both. Where does it seem to be coming from? About what is the tone, high, medium, or low - like break glass high, little sister annoying, or baby crying?
I know this may sound weird, but I read it on another thread. It might be acid gas escaping from the battery. Try taking the seat off to hear if it is in fact coming from that area or any of the hoses underneath the bike.