WR 426 no lights working?

I have a motard wr 426 01 (australian street legal as standard) model and suddenly all the electrics cut out after they flickered for a little while down the street. it still starts and runs fine but and now i've looked over all the wiring for a bad earth as the earth for the headlight brakes indicators and tail light are seperate to the one for the coil ect so the bike runs fine. ive run a 12v battery from the shifter (earth) to the yellow plug straight from the stator and the lights work as they should. how would the lights not run off the rotor but the spark and cdi etc still run. i put a new wr rotor on it about 60 hours ago and it doesn't miss a beat. any clue what's causing it? need a solution/suggestion ASAP thanks!

The stator on your bike has a separate coil to drive the CDI.  So the bike can have a spark and the lights not work.  I would first check the output of the stator.  It should be a black and a yellow wire.  With it running you should see around 14 volts AC and up.  Also check continuity from the black wire to ground, it should be close to zero ohm.  Yellow to ground a little higher.  If you're getting 14 volts and up from the stator then check output of the regulator.  You should see a steady 13-14 volts with it running.  The harness is grounded near the coil, something to check.  

Still no lights and it's time to start cutting open the wiring harness.  Don't be afraid to do it, you can tape it up when you're done.  Sometimes wires chafe and short out or open.  I've cut open a few wiring harnesses and found those problems.   

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