Try giving the guys at baja designs a call. They are right there in san diego, and they not only know what you will need, they will probably have it in stock. They are very nice and easy to deal with, too. Check out their entries in the Baja 1000. They have put together some super trick xr650s that have done pretty well.
You will want at least, a new exhuast end cap, with better flow, made by honda. You will also want to re jet the bike, which is super easy and BD will give you the right jets and instructions in their hop up kit. It also includes a less restrictive boot that goes between the airbox and the carb. You will also want to get a block off kit that removes the smog pump. They also make great skid plates.
I know I am really pushing BD, and I don't even work for them!! They are a great company and I have been nothing but extremely satisfied with their customer service.