The stock Regulator/Rectifier unit leaves a lot to be desired, check that it's not over charging (Should not exceed 12/13 Volts on battery level meter whilst running) - It is possible that the wires have melted if this is the case.
The regulator/rectifier unit is that small, silver box that sits high up below the tank on left hand/clutch side of the motorcycle.
Good luck!
Liam
June 2012