Jimmy,
I heard back from Cliff Naef on your flat spot problems. Here goes:
1. change needle to one step richer. If it gets better, go another 1/2 step by shimming until the problem goes away. If worse, try leaner.
2. What type of exhaust do you have? Is it a Yoshimira? They have a flat spot in that RPM range on many bikes he has ridden and they couldn't correct the problem until the pipe was changed. Yosh makes good top end while scraficing mid-range.
3. Check with GSXR riders, some cams have aninherent flat spot. They may confirm this. Cams may be degreed to extreme top end power at the cost of some mid-range. 4 degrees should be good but you probably wouldn't notice much difference at any setting 3-5.
4. Are the carbs stock?? Try mikuni 40mm flat slides or 41 mm Kehien (spell) They also had better results from the Advance Jet kits with titanium needles verses the Holeshot Stage II (or Stage III may work better). Are the carbs properly syncronized?
5. If the head has been large ported, you can lose fuel velocity at lower RPMs and create a bog.
This is all he gave me, hope it helps you go faster.
Ducati