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XR650R - Please help me identify these wires

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I posted this over in the advrider "XR650R electricity" thread, thought this might be a better place for it:

 

Rewired the XR and I'm down to the stock wiring harness. See attached picture for wires in question.

I've been referencing the this wiring diagram to sort it out and this is what I'm making of it so far:

http://www.xr650r.us/tech/na_wiring.jpg

3xGreen = one from engine cutoff, one from coil and one from ignition control module all go to one side of AC regulator

2xBrown = Here's the confusion, one appears to come from ignition coil and go to ignition control module, but the other? Why are these two spliced together? OEM diagram only shows two brown and they are independent circuits.

Black/red = to ignition coil that I left as is on stator

White/yellow = this one stays capped, I'm running tail light on the DC circuit and Headlight on AC 14 awg wiring harness I built from scratch.
 

For reference, I rewound an electrosport/moose stator. Two poles left untouched (ignition coils), 8 coils wound with 14 awg and the other 7 with 16 awg. I'm using two AC regulators and one DC reg/rec. One AC reg is for stock harness/ignition while the other is for only the headlight (independent wiring harness with relay). DC leg runs through Trusk DSK harness (great harness for $30) to LED blinkers/tail light/brake switches w/battery. I thought it was worth a shot, before sending the stocker out to BD.

 

Any help would be greatly appreciated.

20140817_163501.jpg

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They shouldnt be spliced, one goes to the ICM and one use to feed the stock tailight.

That's what I suspected, thanks.

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they are basically two different wires as Ricky said above. Honda seems to run out of colored wires lol

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