So I went ahead and ripped out my filter box up to the throttle body (not literally).

Under the original intake pipe there was this small box that was connected to the original stock pipe. After I installed my intake I left the 'small box' on the side of my new intake but it is loose and is not mounted to anything. It has a set of wires leading to some other compartment and it has a tube connected to somewhere else. I am unaware what I am suppose to do with this but is this an O2 sensor or what? Let me know. I could probably get pictures if that is neccessary.

 

The picture would help. It wouldn't be an O2 since they are on the exhaust. Could be the MAF sensor, buut I'm not familiar with your engine. Someone with a similar car will be able to help more. Look for a diagram to figure out what it is, there are links all over this forum.