A few more questions

If you are removing the lights, there is very little wiring left. You have the coil pack, the ignition box and the kill switch. That's it. You don't have to install any of the others

Is the yellow wire going to the voltage regulator? It appears to be going that direction in your picture. The VR is the two wire device that is bolted to the frame member behind the airbox.
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No, it doesn't. The yellow (as said below) comes up from the light coil under the flywheel, out of the harness at the airbox area, makes a u-turn and heads back toward the light switch.
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The wire (from the lighting coil) to the headlight switch is yellow. From the switch it goes to the VR (gets regulated) and comes 'back' red for the lights.

re: 'Is the kill switch wire supposed to origonate at where i have it, '

I don't get that part. Are you asking where the kill switch plugs in?

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One wire (black) from the kill switch goes to a ground point at the hi-v coil for the plug, the other goes back to the cdi unit.
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My bike is in more pieces'n yours at this time. I can look at it tonight and let you know. Or, I could look at my manual and tell you, too. ;) You should have one.

I'd appreciate a bit more clarity on your question, though.

RV6 said it right. There's a lot 'missing' if the lights are out.

What year kx frontend? You don't have isolation cones on the bars, do you?

Very interesting... my bike too is more in pieces than your picture. At a casual look I think the yellow goes from the magneto to the light switch (ie. you won't need it). The black wire goes from the magneto to the CDI unit (you will need this one). All the other wires in the system with black or white are striped with another color. I have also removed the lights and odo for MX fender and number plate. I guess we're all taking advantage of the winter months to do our more major modifications. I must be as much of a crazed perfectionist KDX fanatic as the rest of you!

Over here in Oz I havent ever seen snow. I know Im not trying to rub it in but its hard for me to find the time to get my maintenence done. Its either work, sleep or ride.....