Taken from
http://xs650temp.proboards.com/index.cgi?board=Charging&action=display&thread=3461 but I think a login is required so read below:
This is taken from one of Curly's posts, and is one of the best troubleshooting guides we have seen:
1. First charge your battery to at least 12.5-12.7V.
2. Find a really thin feeler gauge like 0.010" or 0.015" and hold it pointed down about a half inch away from your generator cover on the engine. Now turn the key on. If your regulator and rotor are working the feeler gauge should slap the case when the magnetic field is created in the rotor. If nothing happens or the magnetic effect seems really weak then go on to the next test.
3. On the solid state regulator models all you need to do is locate the green wire at the regulator plug and make a jump from it to ground. That bypasses the regulator and allows full battery current to flow through the brushes out of the rotor through the green wire to ground. That causes the rotor to make a stronger magnetic field which in turn causes more current to flow in the stator. If your battery terminal charge voltage jumps up to 14.5VDC when you rev the engine then the regulator or the ground connection for the regulator is your problem.
4. If nothing changes then it's time to check the voltage on the brown wire (It may be black on your bike) at the positive brush with the key on. It should be very close to battery voltage. The brown wire that feeds the brush gets its power from the brown wire at the keyswitch. Check the voltage at the three wire keyswitch connector while it's plugged in by probing from the backside of the connector with the key on. Again you should see the same voltage as the battery. If you do get full battery voltage there then repair the brown wire circuit between the switch and the positive brush. If not then the switch is either bad or the red wire from the battery is not passing the full current like it should. If that's the case then keep going back along the red wire, through the main fuse until you find the source of the voltage drop. No more than 0.3 VDC drop is acceptable.
5. Once you have full voltage to the positive brush re-check the charging voltage to see if you're getting 14.5 VDC or better at the battery when revved to about 3,000 rpm. If you still don't have a charge then do the feeler gauge test again. If it slaps the case your rotor and regulator are working and you can go on to stator checks. If not then pull the brushes out of their holder and use an ohm meter to test the rotor. Measure the rotor first by touching the tester leads to the brass slip rings. Then take one lead and touch anywhere on the engine that's not painted. For the first test you should see between 5 and 5.5 ohms between the slip rings. On the second test between one slip ring and the engine you should see infinity on the meter. Any reading lower than 5 ohms on the first test or less than infinity on the second test means you have a bad rotor. Replace it. If it tests good then go on to the stator checks.
6. At the stator wire connector locate the three white wires. Use a voltmeter set on the AC scale to test the three possible connections between the white wires by probing from the backside of the connector. (The connector should be plugged togeter for this test) With the engine running at idle you should see about 10.5 to 11 AC volts (Not DC) on each of the three combinations of white to white that you make. If you get a very low reading on one or two legs then something is grounding your stator. If you have high readings on any of the legs (i.e. 16-18VDC) then your rectifier is bad.
7. If you got low readings on any of the stator voltage checks then unplug the connector and use your ohm meter to check the stator windings. Check the resistance between the three fabric covered wires (stator side) on the side of the connector. On each white to white connection you should read about 0.4 to 0.5 Ohms. If you get a very low reading on all of the three combinations find the single Yellow wire connector and disconnect it. Re-check your stator resistance. If the readings are now good then the yellow wire or safety relay are shorted. If there is one or more that still read low after disconnecting the yellow then check those legs by touching one lead to ground with the other on the white wire. You should see a very high Kilo ohm or infinite reading. If you get a low resistance check the stator lead pigtail to see if it is pinched by the cases or rubbed through on the frame. If that looks ok then your stator is shorted and needs to be replaced.
And that's about it except to say that dirty connections and worn brushes account for most of the charging system problems. Good Luck you'll find the problem.
The original post is found HERE. Thanks again Curly!
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So, the answer is to unplug the regulator when doing the battery straight to the green wire test. 
