A true CAI would, but not just an open cone filter in the engine compartment. A CAI must pull ALL the air from the outside, not the hot air from under the hood. The original intake box is more of a CAI than the cone filters that are inside the engine compartment, BECAUSE; there is a snorkel (funneling duct) on the the intake box that faces directly front, and gets the outside air, and not the hot inside air.
If you wanted a true CAI, you would have to tube it down low enough to pull the colder air from outside the engine compartment. Or, cut a hole in the hood and scoop it to the intake cone, OR, actually get a Snorkel intake system for the Jeep. I have seen one with a snorkel, it does not look all that bad.
Exhaust? Got to be careful, changing back pressure changes the torque curve. If you free up the exhaust too much, you lose low end torque, to a higher RPM range. A good muffler will help...