No start! wiring help.

Hi All! This is my first post here and am excited to join the FZ1 Community. I have just bought a 03 fz1, it was abandoned and recovered by a towing company and I was the lucky one to pick this up from them real cheap. Says it has 13000 miles and very minor body damage (pics to follow). I will be starting a build up thread on it and hope to use this forum as a voting both as to what mods and parts to add as it comes back to life. But before that can happen i need to get it started! It did run when i bought it i did do a minor test of it around the block, but when i got home i made the mistake of wiring the ignition wrong and now it wont crank.
What I did: The 4 wires that run to the ignition were wired all together, i was then told that the 2 power wires and the 2 blue wires are to be separately twisted together.
Symptom: Bike is in neutral but no neutral light on dash, Pull clutch in and still nothing. Does not matter if kick stand is up or down.
Question: Were do the blue/black and blue/yellow run to? What could have been damaged by wiring them to a power wire?
Trouble shooting so far: I have jumped the starting relay and the starter is good. All fuses have been checked all good. Checked Bulb in dash.
I will be checking all switches tonight (neutral, clutch lever and kick stand) with a multi meter and will post the results. Could i have taken out the IGNITOR UNIT 5LV-82305-30-00 or RELAY ASSY (5EB-00) 5EB-81950-20-00 ? Refer to 2005 FZ1 - FZS1T Yamaha Motorcycle ELECTRICAL 1 Diagram and Parts for components and locations.
 
So I tested all the switches and found that the neutral switch was bad as well as the kickstand. I will be bypassing the kick stand switch and installing a new N. switch. I also checked my brake switches and found the handlebar switch bad so will replace. Does any one have any suggestions on what i could replace the master cylinder and brake switch with. It got damaged when it was laid down and i need to figure out if i want to fix the current unit or replace the lot.
 
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