Yep Matt sounds right to me, check your airbox and filter assembly (like Matts post shows) and make sure you have all the correct parts. Your bike will run significantly different if your missing any of the boots or pieces that cause even the smallest gap.
Also all these boots do shrink with age, so it will be really hard to slide them onto there correct area. I found spraying the boots with carb cleaner will expand the boots enough to fit them on tightly. Make sure the boot clamps are slid all the way forward and completely loosened before attaching, I used to loosen them so they could obviously slide back, and forth on the boot but then when the boot needs to expand for attachment it totally stops it because it's not loose enough.
Hope that helps, let us know how it goes.