May i interject? I am personally going a SLP single pipe with a can. Also there are products (i think its called and air horn) from SLP that allow the engine to breath better. With this combo you will have to do some type of clutch modding, not too much. SLP will have all the specs and carb details for you. I strongly recomend that what ever you decide taht you go through SLP. The have done all the research and will tell you exactly what works for your sled. There is an atricle in this months snotech magazine that covers this on a 03 800 RMK. Its pretty much the same sled as yours. The weight reduction was around 11 pounds and the horse power increase was about 11-13. Your engine stock puts out about 120-126 hp. Total upgrade costs $500 (give or take) and total hp is somwhere around 130-138. I know a guy who did this with reeds and a boost bottle and he is now at 138, however he did it with a 98 so he started with a little less.
Twin pipes are good but i wonder if their is not enough back pressure and you would just be shortening the life of your engine. I can check my racing manual for jetting at that altitude. however that is at home at I am dicking off at work.