With the rotor/field coil being the "weak link" in the 650's, that'd be my first suspect. They've been known to "open" when hot and then start working again when they cool off. Also, I've never gotten the same resistance reading at the coil itself as at the wiring harness (going through the brushes). With the engine running, checking resistance is impossible; the reading will fly all over the place.
With my understanding, if the stator had an open in one of the windings (three-phase, three windings), the system would still just barely charge. I would suspect even an open/bad rotor winding would be able to charge the battery and run the coils if it doesn't also have to run the head light. I would do my next ride and test with the headlight fuse removed.
I haven't read through the
entire thread for a while, so I have to ask if you've replaced the regulator? That would be one thing that could easily quit working with heat.
Here is step-by-step of what I would do. First thing's first, you'll need two wires with alligator clips on each end. They'll need to be long enough to reach from the battery terminals to the field coil connecting block under the seat. Note that all of these tests will be with the engine running, fully warm and in failure mode.
You'll first need to get the bike to operating temp and in failure mode. Once the low voltage situation is verified, disconnect the alternator's connector under the seat, and connect the alligator clips to the pair of spade connectors inside the connector. The goal here is to give the field coil
full battery voltage.
If your field coil is shorted out as mine was, the light will dim and the engine will probably bog down. If this is the case, disconnect the wires quickly; your rotor is shorted and can start melting wires rather quickly. If nothing obviously bad happens, continue to the next step.
The first option is to pull the rotor spade terminals out of the connector (they'll just "pop" back in when done) and plug the connector itself back in. This way you can keep battery voltage across the rotor via the alligator clips,
and the stator's three-phase output stays hooked up to the rectifier and therefore the battery. This will only bypasss one component (the regulator). At this point, check your battery voltage vs RPM's; voltage should go up with engine speed. Note that with no regulator, the voltage should simply keep rising as RPM's go higher. I've seen up to 18v across the battery during a short burst of high RPM, so be careful as you don't want to melt your coils, burn out bulbs, or boil your battery (don't hold high RPM's/voltage for too long). If the system passes this test, than your rotor/stator are good but your regulator is bad and needs to be replaced.
If the previous test failed, the next step is to check the AC voltage coming out of the stator as-is (with the connector completely unplugged, engine running, and battery voltage across the two rotor wires). Be cautious here, as with full battery voltage on the rotor and no load on the stator, voltages can get decently high (I've read of 100+ volts). If the voltage goes up with RPM and all three voltages are pretty close to the same, your rotor and stator are both working correctly. If not, you've got a problem in one of the two components or the wiring to them. **NOTE: The three wires will be outputting AC voltage (NOT DC) and your multimeter must be set on the 200v AC scale.**
If after doing both of these tests, there IS voltage across each of the three stator terminals, your rectifier is fried. Since it's a one-piece R/R unit, I suggest using the Ford regulator and three-phase bridge rectifier combo that I've written about.
If all of these tests fail, I'll have to devise an easy way to test the rotor/stator and wiring when in "failure mode."