Missing part of the airbox - running too lean?

On my never ending quest to get my bike to run better, I have a question concerning the stock airbox. The airbox itself is there, along with the lid, but the rest of the stock intake setup is missing. I wasn't aware of it until I was looking at a parts diagram online and saw the extra parts that sit under the seat. From what I can tell, there is a silencer of some sort just above the battery that looks pretty restrictive, and a rubber boot that connects this silencer to the airbox.

Since I am missing the silencer, could my carbs being getting too much air? The only mod on the bike performance wise is a MAC header, and I've had to rejet a few times to get it running as good as it is now. It still seems lean to me on colder days, so I thought this airbox deal could be causing it to run lean. Should I try restricting the air some to see if I can tell a difference in performance?