I would do it in this order
1. Air filter, Toomey 2 into 1 or a pro design plate with either a foam filter or a K and N or two K and N filters. The stock air filter sucks and will damage your engine.
2. Pipes, depending on your riding preferences there are many choices. CPI's for the dunes along with Toomeys. Pro Circuit makes a great all purpose pipe, for both dunes (wide open) and trails, and FMF Gnarlies for the woods/trails. They have alot of low end power
3. Better rear tires, the stockers just spin. After your pipes the most noticiable improvement is tires in my opinion, until you get her ported and polished.
4. Cool head with smaller domes, 21's at sea level is still pump fuel, 20's should be a mixture of race and pump , anything under 20's you should really run straight race.