Before you spend any $$$ on other mods., I would highly recommend you clean the backside of the throttle body and add a catch can. There are many different types/prices, so you can do a little research and see which one sounds good to you. Many of us use the Billet Technologies unit (~$100). This is what I have on each of my Hemi vehicles.
As far as the exhaust goes, it's your choice. It should be 3 in. and have a resonator of some sort, or you'll likely get some droning when the MDS is active. The weak point in the exhaust is the "log" type exhaust manifolds, not so much the rest of the system. Consider getting some stock SRT manifolds/headers or, if $$$ is a factor, switch from the stock logs to the LX logs. Here's a thread I did on the difference: http://www.jeepgarage.org/f5/a-better-exhaust-system-for-the-5-7-wk-19490.html
As far as the CAI goes, IMO, save your money. The stock airbox flows more air than the engine is capable of processing. You can improve it by ditching the stock silencers, remove the drain cup at the bottom of the airbox and add a tube leading to somewhere behind the grill (see attached photo), install an AirAid Jr. or SRT tube from the airbox to the throttle body and, finally, add a good high performance air filter element.
A little info. on lowering your WK.....I've lowered mine with Eibach SRT lowering springs and SRT sway bars. I've also switched to Bilstein struts and shocks. I handles like it's on rails now. I've also installed an SRT front bumper. With this setup, the only downside I can see is that with the SRT front bumper, you need to be careful going up driveways and over bumps. I've had this setup for about 2 years and have scraped a few times and bent a support bracket once on a cement parking stop. If you keep the stock front bumper, you shouldn't have a problem, and will love the suspension. One other thing, the ride is more firm too.
Regarding the tuner, I have both a Superchips and Diablosport Predator. Again, it's your choice, and depends on what you're after. Both have their advantages, and would be outstanding if the good features of both were combined into one. The Diablosport allows you to update your PCM/TCM CALID flash files, and gives you more flexibility (adjustable) with regard to WOT fuel mixture and timing. It will also allow you to have custom ChipMaster Revolution (CMR) tunes set up for your particular vehicle. I have found that it also delivers slightly better fuel economy and performance. IMO, the best feature of the Superchips, by far, is the add-on (~$40) Advanced Transmission Tuning (ATT) Application. It allows you to have complete control over all up/down shift schedules, as well as torque management for both light and wide open throttle. You can completely tune out almost all the lousy features of the stock transmission. Throttle response with the SC is also better. For these reasons, I use the Superchips more than the Diablosport. You wouldn't know it is the same transmission. The DS only gives you limited control (up/down shifts for 1, 2, and 3), but does not give you any control over torque management.