You will need to jet your carbs for those pipes. While your at it, I would swap the stock filter for a K&N just b/c they are 10x better. If you run with no lid, run outerwear's. It will help when going thru puddles.
Keep in mind that any time you make a mod that has to do with fuel/air ratio, you will have to jet accordingly.
As far as a cheap mods, gearing for trail use is a good. I personally would put a timing plate in and deck/shave the head. Thats a great bang for the buck. The list of mods is endless. It really all depends on when your happy with it. Do one mod at a time until your ok with the performance.
Edit: Like Shogs said, tors can lead to big issues. Take all that off.