I will have to check one of my bikes, but I don't ever remember seeing only 12 volts out of a stator, even at idle.
With a previous post, I tried to make sure you were checking the pairs properly, now I guess I will have to stop assuming and ask you directly ... are you holding the engine at 5000 RPM? We need to reduce the number of variables here. The factory manual calls for that speed, all of the testing that we ask for also assumes that speed is used. Stator output is directly related to engine speed, so please use that engine speed.
If you have read any of the manuals or tutorials on this subject, you should know that the stator output should be in the 75-90 VAC range. You state that you had 12 volts, "So I took about a 25 minute ride." Knowing that the output is about 1/6 of what is needed, you decided to take it out for a ride?
My interest in supporting this project could be fading rapidly.

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