I would have been inclined to return the guitar, Yamahas are normally solid as a rock, whatever price point they are and loose electronics sounds like someone has been messing around with it. Was it new?. Assuming that there are no shorts in the circuit, neck and middle will always be lower output than the humbucker and perhaps the slightly higher rated pots may be contributing to that. As to the tone issue, perhaps the taper is incorrect. As you can tell, I'm no expert and this is the best I can come up with.