What is the bike doing right now with those jets in it (other than smoking)? Hesitating, sputtering, backfiring? When you put the stock airbox back on, what kind of filter are you running and are you running with the lid on or off?
If you're running the stock air filter I can imagine you're probably starving for air...A good setup to run with the airbox is a K&N pro-flow kit and cut 1.5 inches off the back of the airbox lid. By doing that, you get a good amount more air and still protect your filter from mud/water splashing on it...that is if you don't bury your bike in the mud/water. Your jetting sounds close to what it should be, I just think that the stock air setup isn't allowing enough air for your bike to breathe, especially with having pipes and reeds. Let us know what she's doing and we'll get you where ya need to be
Oh yeah, welcome to the HQ!!