My suggestion for your first attempt would be to build a "parts bin" special.
Find an old frame from something fast (old GP bike perhaps), preferably with swingarm and linkages. Find a good motor (Something simple but effective, a big single or twin, Not FI), Make it fit (you'll have to make brackets, etc). Get the best forks and shocks you can find. Make linkages and a custom triple clamp to fit. Get some good, suitable wheels (If you're able, go Marchesini, Marvic or similar. Get some good brakes, either go custom, or find some second hand Brembos or similar. Custom design the pipe (easier on a 4 stroke), Custom design the fairings, ducktail, etc to suit your build, the pipe design, etc.
Custom design/make your rearsets, shift linkages, clipons, pipe brackets, fairing mounts, etc
Building a track day bike is a lot easier than a street bike (I don't know how you go about roadworthys, compliance in the US. It may not be an issue) Get aftermarket indicators, brake lights, etc (if necessary), Make them fit.
Become very good friends with someone who has a mill, lathe and grinder in his workshop. Spend more time designing brackets, triple clamps, clipons, etc, and get someone else to make them to your spec (Until/Unless you are capable of doing it yourself)
Use the best materials you can get your hands on. Chrome Moly tubing for pegs, bars, axles, etc. Heaps of carbon fibre (find the Mythbusters episode where they make the flying backpack. Jamie makes the rotor shrouds in foam, and covers them in Carbon Fibre. Looks Tops, light as....... a really light thing!).
This way, you'll learn quickly what needs to be done, and the mistakes you make will be less costly. You'll still have a one-off machine, that'll suprise people with it's speed and agility.
Good luck. Post regular reports. it'll make good reading, and we might be able to help along the way.