I have 95 Yamaha Warrior quad. I am putting a new magneto on and the old one had a green, blue, yellow and red, and out of the stator had a white a green and two reds. From the CDI box I have a green, blue, yellow and red. from the stator and coil is a white, a green and two reds.... and the plugs are not compatible. It is confusing to try and match up wires now. Anyone able to tell me? I think i can figure out the whites, but the rest just don't match in any way. The original parts are not available, and replacements are a different maker.
The original had a blue and red, and a brown and a green wires. Yep, it is confusing
Perhaps there is a replacement on there now, and I need to use the original diagram to match it up somehow? The diagram I have found is small and difficult to read, but I have it.

 

There is something a bit suspicious if the wiring plugs don't match on the new stator as, if it is supposed to be for a 95 Warrior, no matter who made it, the wiring plugs should match. Yamaha had a habit of making weird stators, but normal ones have three phases going to the regulator, a separate power coil, sometimes earthed, for powering the spark, so wire(s) go to CDI. The small coil on the outside of flywheel is the pulse coil, providing a timing signal for the spark, on Yams this is usually two wire and they also go to the CDI. Careful checking of what colour wire comes from where on both old and new stators, should enable you to sort out which wires should be connected together.