Easy answer to your question: YES, you can mount the PCM without the box.
Now, to get a little more complex,
This topic is a very very popular one, and you can find all the information you need by utilizing the "Search" function of this website.
First, decide what type of intake is for you: CAI (cold air intake) or FWI (fenderwell intake)
Secondly, decide if you want to DIY (Do it yourself) or buy a produced piece.
Gook luck and happy modding!