The box in the middle is the resonator to reduce drone. I yanked mine, plugged the hose with a pvc cap and clamp. Haven't noticed anything annoying, and it's been a few thousand miles.
About the air filter. Like was posted, it looks like something has to be moved to get anything decent in there. Or there is this other guy that went up with the hood. Check it out here.
Rigs
I am thinking about getting a hood out of the junkyard and fabbing something up, putting a 6637 filter where the stock box is. I need to get the filter to see exactly how big of a bulge or scoop I will need.