I would have to agree with geo on the fuel controller, it does make a nice difference in midrange and a little on top. I have also found that replacing the head is a great improvement once you have a controller. I have ran Bikeman's 6000+ head with excellent results, but if money is a big deal, you can pick up an 2008 Dragon head (prior to the update) for next to nothing. Check your squish clearance with the 08 head and have it cut to give you .068-.070 clearance if you are running above 6000ft and pump gas will work.
I know I will likely get some comments about this but IMHO the stock exhaust is tough to beat unless you are willing to spend a ton on porting, head, reeds and clutching also. I am not saying you won't see some small gains with a pipe, stock cylinders and head, it just gets expensive with the clutching and controller added in.
The only other thing I am a big fan of is the Team Tied driven clutch. It is very consistent thru the day in changing snow conditions and altitudes.