I would go back a step or two. The service manual extract posted in reply #17 illustrates taking a no load AC voltage measurement, across the three yellow leads from the stator, with the engine running at 5,000 rpm.
The no load means that the three yellow wired connector, from the stator to the voltage regulator, is disconnected / pulled. I would imagine that this where you took the resistance testing readings from? I'm not sure if there is another connector in between the stator and the regulator. And if the stator wires are a different colour as explained in #6, then those are the wire colours to test.
Anyhow, if you don't measure any AC voltage at this point and there is not another connector in between, then I would safely say that either the magnet orientation or the stator is the cause of the failing to charge.
Please report back on the AC voltage reading results.