Your Alternator is made of a stationary Stator (set of coils) and a spinning permanent magnet (rotor).
To test your alternators condition, disconnect it at the plug. There are four wires in the 6-place plug: Red, White, Yellow and Light Green with a Red stripe. Using a multimeter on OHMS, check between the Red-White wires, Red-Yellow wires and, White-Yellow wires. The OHM reading should be very low (.5 to 10 OHMS), a virtual short.
Then test resistance of each of these wires to ground. The readings should be very high or open.
If all of these tests are good then your alternator is physically good. If any of the readings between the wires is high or open, or there is anything other than very high resistance to ground, one or more of the windings in the stator is broken or grounded and you're going to have to replace the stator.
To test the operation of the alternator, crank the bike and turn on the headlight and shine it on a wall. notice how bright the light shines. Then turn off the engine. If the headlight gets dimmer then the alternator is charging. DO NOT disconnect the positive lead from the battery with the engine running. If the alternator is working properly this will cause the regulator to drive the alternator to maximum output and might fry your rectifier, regulator, lamps and/or any other electronic devices and then troubleshooting will turn into a nightmare!!!
My $.02.
FMTL