When I was running the stock harness I built a bracket to relocate the rec/reg just above the countershaft sprocket area (the same small void where the kit oil can mounts). The other wires got zip tied up tight and tucked away cleanly.
For a while I had the rectifier zip tied to the inside of the race fairings. Now I have the kit catch can which relocated to above the front sprocket, like DDK732 mentioned, you can make your own bracket to mount there, there is even a threaded boss there you can use.
The kit harness is reasonably priced and makes life a lot better. And not just a little better. A LOT better.
What Mike said. I had all my wiring stuffed under the airbox and lengthened the wires for the rectifier and mounted it where the others did. Th airbox was a TIGHT fit and I was afraid of wires chaffing with being so tightly packed in. The Kit wiring harness is a must if you aren't going back on the street from both an asthetic and functional standpoint.
If you don't want to hack up your stock harness I still have mine with the lengthened rectifier wires if you want to buy it.