Problem solved
 

After doing some plastic welding to get the "ear" back on the fairing, I decided to apply the welder to my "point of impact". I successfully pushed the fairing in to allow clearance of the the throttle tubes, and I don't think it will look that bad when it all painted.

I am painting now, and I have to wait for some Master cylinder parts before I can finish up the front end. Once the tank is done (by next weekend) I will be able to go out for some "tuning" rides.

I guess next week got pushed out a bit. But today I got the tank on and put some gas in it. She fired right up after a few cranks. What a bike!

So I am still in the process of painting the plastics. I am going with Flat Black Rattle can for an intended Hot Rodder/DIY/Rat Bike effect. Did you know it is damn hard to make a glossy paint job flat? I will let you know when I figure it out, but so far, steel wool is the best option.

But I got the tank on and the bike running. New EBC HH pads on the front, fresh bearings in the head, fresh brake fluid, and new detent spring and arm on the shifter (stock spring).

Some notes on the progress:
-When filling a new brake system with new fluid, it can be difficult to get the fluid down to the calipers. I took the shop vac, and adapted the crevice nozzle to a piece of 3/8 tubing. Hooked the tubing to the bleeder valve on the caliper, opened the valve, turned on the vacuum and squeezed the lever. It took a couple minutes per side, then I properly blead the brakes.
-I discovered after not noticing it when I took it apart, that there are only three function screws on the gas cap. The two next to the hinge and the one at 12 o'clock. The rest are dummies, don't bother removing those.

Test Ride:
I just rolled around my hood since I wasn't 100% sure about anything, and I only got into third and fairly slow speeds. But the brakes feel awesome. I am using 954 calipers, and an RC51 MC. I look forward to seeing how they work at speed, but definite stoppy potential now. I also noticed immediate difference in shifter feel from the partial shift kit. The shift seemed crisper. A little quicker, not sure if the throw is shorter (it kinda feels like it), but certainly more positive engagement.

I don't even know where to start with the suspension set up, so I have to do some research on that. More reviews to come as I get her up to speed.

After a couple more rides around town, I have to say that this project is ending as "well" as it began for me. It appears that something is tweaked, and I am guessing it is the lower triple clamp. The upper triple is clearly pointing a bit left when I am riding straight. I guess I have to pull it all apart again. That's the way it goes when buying stuff on eBay.

As far as fit and function are concerned, I am fairly happy with the way it turned out. This is not a conversion I would recommend for you average street rider. It is definitely a PERFORMANCE upgrade, but there are definite compromises with regards to ergos and street handling that would not be satisfactory to me if I did not take it to the track. If I were to put a superbike bar on it, it might be a little more street friendly.

I have yet to really tune the fork or even take it out in to the twisties, so more feedback to come.

I can't believe I never finished this thread off.

Well, it has been a year and a half since I finished the upgrade. I painted the bike flat black and enjoyed it for a while. Now my neck hurts and I stopped going to the track. I am doing a street fighter thing to it now. Preliminary testing has shown that this bike should have been a naked fighter all along. With risers and dirtbike bars on it, it looks and feels awesome. I will throw a couple photos up here to show the progress!