Well, based on what i saw in the box o'parts that comes with the bike, it was previously running pods, so no airbox. The 4-1 is also not the stock exhaust. It appears to be a Mac.
I am going to track down a stock airbox. I haven't decided what to do about the exhaust, but the vision I have in my head for this bike includes a 4-2 exhaust rather than the original 4-1.