Every time I try to start my bike, the main fuse blows

You aren't being clear enough about what has to be connected to the switch and what position the sw has to be in before it blows. The idea is to disconnect and reconnect everything in steps to the bad wire and when it blows you'll know where the problem is. Then take the thing that blew it apart and try to fix it. Like maybe the kill sw has a short to ground inside....
 
I connected the wires from the kill switch together, the brown and the red/white, and it blows the fuse as soon as I turn the ignition on. Is there a way I can bypass it?
 
no that is just telling you that the short is either in the brown accessory circuit or in the ignition circuit, if you can connect the red to brown without the r/y and it doesn't pop the fuse the fault is in the r/y ignition circuit, the ignition gets its power from the brown so disconnect it, if the fuse still blows the fault is in the brown
 
Now I'm a little confused, I thought the ignition circuit gets power from the 12v red wire. I was also under the impression that the red/yellow sends power to the headlights. I traced the brown wire from my kill switch and it meets up with the brown wire from the front brake switch then goes straight to the ignition switch? The wires all look good though.
 
it does but it goes thru the kill switch to get it
 

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Now, I ran the brown to the red/white and turned the ignition on with everything else attached and it was fine. I attempted to kick start it a few times but it's cool out today so I just pressed the start button instead and it started up for a second, then blew the fuse. I did run the red wire to the brown and it didn't blow the fuse. Where should I go from here? This is really kicking my butt.
 
check the red/whites from the coils up to the headlight shell .. bypassing the kill switch, that is plugging the red/white that comes out of the main loom directly into a brown off the key switch
 
Just checked the wires, everything looks clean and yes, I ran red/white directly to brown to bypass the switch. Still blowing fuses though, just after she gets firing too.
 
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