If you try Steve's test, make SURE you have GOOD connections to the jumpers and that they can't become disconnected if you bump them.
If the jumpers become disconnected while the engine is running, you are running without ANY battery in the system. In addition to the other things it does, the battery acts as a filter to smooth out the fluctuating DC supplied by the R/R.
Without the battery high voltage spikes enter the system.
There are previous threads where people have had issues occur where batteries became disconnected while the bike was running, and then had the ignitor blow.
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Also, I thought of another test you can try.
This is to try to isolate if you have an issue with one of the phases, or it is something else.
The idea is to intentionally run the bike on only two phases at a time.
Disconnect one of the yellow wires from the stator to the R/R, start the bike and see how it charges (voltage with light on, voltage with light off, both at 5000 rpm)
Now connect that one back up, and disconnect a different one. repeat the charging test.
Repeat for the third wire.
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If all three tests provide equal results (whatever they are) then it is not a problem with one of the phases and you will need to look elsewhere than my previous suggestions.
If two of them provide one level of charging (probably worse than currently charging) (running on one bad and one good phase)
and the third is different from the other two (probably about the same as it runs on all three phases now)(cause its running on two good phases, and the bad one is the one you have disconnected)
then you have isolated the problem to being a problem with one of the phases.
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