It feels like my hips are rolling under and putting everything in a bind. I'm fairly short 5'6" so that may be magnifying the problem.
I would bet on the reach to the bars then, aside from your body just not being used to the riding position.
Try cruising with one hand on the throttle and sit back and upright as much as you can(as if the bars were taller and closer to you). See if that's more comfortable.
The new Image seat Twotonevert recommended may/may not help, again, some love them some hate them.
That seat is thinner than stock. It will put you against the tank, as well as stuck in that position.
You will sit noticeably lower so your knees will be higher, and that will put your hips in more of a bind.
Try folding a towel and putting it on the seat, essentially making the seat taller. Not so great for a short rider, but will answer some comfort questions for you.
If you can sit upright on the seat comfortabley, and then have hip pain when you lean down to the bars, then the reach to the bars is the problem.
If so, Heli-bars will raise the bars .75", and the angle of the bars changes too. The ends of the bars are higher.
You can combine them with .75" spacers and still have cable and windshield clearance.
The other bar option is different top clamp with a dirtbike style handlebar.
Adjustable rearsets will move so that your feet are further back, and/or higher, usually up to an inch in both directions.
The Buell peg mod will lower the pegs an inch, and there are aftermarket pegs that will lower them 1.5".
I tried all these mods and went through 5 seats on my gen2 after a back injury made it very uncomfortable(I'm also 5'10" and flat foot the Busa easily with a slightly bent knee).
The best one was trading my Busa for a B-King, same power and a lot more comfortable
Hopefully you won't have to take that far.
to the oRg 
hayabusa gel seat review and get 1001 responces. 
