I am certain that since it came from the factory its reasonably important... but Ill ask anyway. There is a part designed for air intake that goes from the upper fairing directed to the air box. I dont have the two pieces anymore and the new fairings dont have a spot to mount one.
So I guess I have multiple questions...
Will it run alright without them?
If I wanted to pick up a set, where would I look?
Could I make my own modified version to have the same function?

 

If you are talking about the hole on the side, it is there just for looks mainly. The intake tubes, I believe, drop down over the frame in the front. I am not 100% on this though.

 

^^Im asking about the black piece, intake tube I guess, that screws in right after the holes on the upper fairing. Do I need that part?

 

The black plastic piece that goes behind the hole in the side fairing, deflects air to in around the sides of the airbox and go out of the area below the carbs. the airbox intake is up by the head stock. Not critical, I think, but shows Honda's attention to small details. Your fairing piece is race fiberglass and racers didn't add the deflector piece.

 

^^awesome reply, thanks man. Sounds like I should stop worrying about it then.