Bump! I'm not going to say I hate 125's because I have never rode one. But my first bike ever was a CR250. I had a few small wrecks, but then I could ride the hell out of it!
If you NEVER plan on riding in wet conditions, ditch the box for sure!! Ditching my airbox was the first mod I did. The engine breaths sooo much better. Just make sure to properly re jet after taking it off.
I'm with Rnbrad and the stainless idea. I would get rid of my Cpi's today as soon as you can fab up some stainless rockets! (my Cpi's have only been rode on 3 times) Good luck! Keep us posted!