I take it the 03 models have the wiring running under the carbs?
my 06 runs down under the motor, so only slightly different
trace the wires from the cover of the rotor (alternator) to the joiner before the regulator, run a multi meter across the 3 wires in turn pairing them up, on the rotor side, start the motor and rev to around 4000rpm and and note the readings, this is where you should get a reading of between 60-70 volts, if its lower then you know where your problem is, if it is between that, then it maybe your regulator