Lucky, I'm going to partially disagree with you here --
Travis - i think that while it is easier for us to give tuning advice if you're running a stock setup, you don't need an airbox. If your bike runs strong when you 1st start it, but then wants to bog down after warming up, you can probably make a few minor adjustments to the carbs to get it running consistently no matter the operating temperature.
however, you will want to educate yourself as to the basics of carbs and how they work before you go doing anything drastic.
My CB550 has different carbs than yours, but was doing the same thing (because as lucky said, it was running lean), and I was able to simply adjust the air screws on the carb bodies to get it running steadily even when warmed up.