Alrighty! I figured out the resolution to the R6 controls and the throttle cable being too long. I am using 2007 R6 controls which have a seperate throttle tube from the switch box. Somehow(luckily) I lokst the throttle cables from my R6 assy. No big deal, the whole shebang cost me $10 on ebay. With the 07 as with earlier R6 controls, the cables are too long. Earlier R6 setups can be adapted to use the FZR cables, but the newer ones cannot. Since I needed to order new cables anyway, I went to my old friend ebay and bought a YZF600 throttle assembly for $15. It uses the same type of setup as the newer R6 in that the throttle assy is seperate from the switch assy. It also should not have the cast in metal pin to seat the assy on the bar and the cables will be a more appropriate length for the FZR. I just ordered the parts and they should be here hopefully next week and I will take some pics and document it properly. So for $25+shipping, about an hour with a soldering iron and shrink tube(Thanks Thatkid! Your Wiki writeup was very helpful!!!) you too can have modern switches with appropriate length cables with little to no other mods necessary. Plus I personally like the slimmer look of the switchbox without the throttle built in.
To Do Checklist:
R1 igntion cylinder -
Buy/install headlight -
Replace ign coils and starter - Parts in transit
Mount Overflow bottle - Parts in transit
Mount speedo - DONE
Mount Speed Sensor - DONE
Tune/synch Carbs -
Buy integrated taillight - Parts in transit
Fab front seat hold down tab-
Make can mount - DONE
Custom Midpipe -
Add relay to low level sensor -
Wire liscence plate LED -
Decide where to put liscence plate

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YZF600 Throttle - Parts in transit
Need new chain guard -
Fab fuel pump bracket- DONE
Replace misc hardware with black ones -
Mirrors - Parts in transit
Make new dogbones-
RIDE THE TITS OFF OF IT!!! -
Damn, my list keeps getting longer. i finish one thing, and add two more...