Rob,
Maybe this will help a bit until the resident genius weighs in... It's been a while since I've seen an MT250 stator, but according to the wiring diagram there should be a coil with a white/yellow wire and the other coil end grounded (headlight coil, straight AC to the bulb through two separate switch setups) wound with fairly heavy-gauge wire, another coil with yellow and pink wires (AC to the rectifier for battery charging and all bulbs other than the headlight) wound with similar wire, and the ignition source coil (black/white wire, one end grounded) wound with more turns of finer-gauge wire.
In this circuit, it shouldn't matter which direction the coils are wound. I don't know if you use the headlight much, but if so this might be an opportunity to rewind the lighting coil for an alternative headlight (LED, 12V, etc.) if desired.
Perhaps you've already done so, but I would take a resistance reading from the lighting coil ground to the headlight bulb socket. There's a lot going on between these two points, and if you see an open circuit the coil won't matter much.
Ray
_________________ '74 CR125M (175cc), '75 MR175, '82 RM250Z, '08 YZ250F, '14 Zero FX electric, '14 Zero MX electric, '18 Alta MXR electric
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