Here's a step-by-step that I went through to fix my alternator problems.
1. Measure field coil (rotor) resistance. If below 4 ohms or above 10 ohms, replace the rotor and start over.
2. Verify that the brushes contact the rotor.
3. Start the bike and connect battery voltage directly to the field coil leads.
4. Test voltage.
--If battery voltage rises as the engine revs up, your field coil, stator, and rectifier are all likely to be good. Regulator or wiring likely at fault. Continue to #5.
--If battery voltage stays steady or drops, either the rectifier or stator is bad. Skip to #6
5. Reconnect all leads and verify that the regulator has both a ground reference and a positive voltage reference.
--If not ground reference or positive voltage reference is missing, check wires and then start over.
--If ground and battery voltage is present, replace the regulator and then start over.
6. Switch your volt meter to AC volts. Check for voltage between all 3 yellow stator wires with the harness disconnected (ignition on, engine running).
--If you get 13 or more volts (I've seen up to 50v) across
all 3 wires, your stator is good. Replace rectifier and start over.
--If you don't get at least 13 or more volts across all three wires, your stator (or wiring between the stator and the rectifier) is bad. Check wiring; replace stator and start over if the wiring isn't at fault.
7. Disconnect the stator harness. With the ignition off, verify resistance between all 3 yellow wires from the stator (check your manual for correct resistance readings.
--If your resistance readings are out of range, replace the stator and start over.
--If your resistance readings are correct, you've effectively checked everything that I can think of, and there has to be a wiring fault.
8. By now you should have an idea what is wrong.