I've taken those 3 clips off many times before and every time I hated it. Basically they have these 2 spreading clips on the backside so when they get pushed in they lock so you can't pull them out. What you have to do is take all of the other screws off and let it hang out. Get under the car and reach up to feel the clips, there'll be 2 corners of the clips that bow out. With large pliers or adjustable pliers, you have to squeeze the 2 spreading locks in and push or pull on the clips. Its really hard the first time, took me almost 30 minutes to take all three off the first time.
As for that black tube for the CAI, yes, if you remove that you can run pipes for CAI through there. You also have to remove the that white resonator box too. Theres a sticky for CAI DIY. I did it for my own car too, its not too hard if you're good at working with our hands and have basic DIY know-how.