Is it possible you could have switched the running light (not headlight) wires with the brake switch wires up front? On my bike, they are close to the same size plugs.
To tell you the truth, you just need to go through everything with a volt meter and map it out. I pretty much rebuilt my entire harness when I switched to DC and made a new wiring diagram for it. The wiring on these bikes are actually really simple, but can seem confusing when its just a big jumble of wires.
I don't know if you have seen this diagram or not, but its not too helpful anyway:
http://www.gasgasrider.org/gg-wiring.jpg
Here is the diagram I made for my bike, not pretty, but it works. Keep in mind I DC converted it and have a reg/rec and a capacitor. It may help with the tail light and switch wiring though.
http://i306.photobucket.com/albums/n...gramGasGas.jpg