Engine won't run without at least minimally charged battery. My guess is, when rpm drop to idle, battery voltage drops under 11, engine dies.

My 5 cents: you have 100V AC between all 3 combinations of yellow wires? That's good.   Stator is tested by measuring AC output (ENGINE RUNNING) between Y1-Y2, Y2-Y3 and Y1-Y3 (All three need to read some 60V at no load, and.... hmmm I forgot how much with load   ) and Ohm resistance (ENGINE OFF) between Y1-GND, Y2-GND and Y3-GND (must be infinite)
Once you past that, you still only get 12.3 DC on high rpm? Not good.  
Manual states voltage has to be 14.5 at battery terminals at 5000rpm (SCREEEEAAAAM) Hmmm, I say it should be around 14-14.5V at any rpm above 2000. Mine does, there's no reason why all other's wouldn't. Either you have a 2V voltage drop (bad connection) on the rectifier jack (take apart, scrape, clean, reconnect), or your Reg/Rect unit died.