Hellwig front & rear sway bars will help w/ handling.
As far as tune I recomend the Diablo I2(also a pcm if your have a 2015 or newer) w/ a Jay Greene custom tune. The tune from Jay is what really woke my truck up the most.
As far as exhaust there are a bunch of different kits to choose from. Depending on if you want to go w/ headers or not is what I would base your muffler choose on. Stock manifolds I would choose Carven or a smaller Magnaflow. W/ headers I would go w/ a larger Magnaflow. If you want headers the JBA 1 3/4 long tubes are the most common & best bang for the buck.
As far as intakes everyone chooses b/w S&B & Vararam. I have the S&B & like it. I dont like the Vararam. They have fit like crap for yrs on the 3rd & 4th gens. An intake that you have to shut the hood on to get to fit right is not something I want to spend money on.
The Pedal Commander seems to be the latest fad right now. It is a throttle booster that bumps up the voltage from the pedal. A tuner has a throttle booster but not as extreme apparently. I personally just push the pedal down & dont need the extra umph in a rc but can see how it will help on a 4 door 4wd that is heavier.
W/ a tuner you can pull the clutch fan off, run the factory a/c electric fan & install a 180* t-stat and regain a little more power that would otherwise be lost through the clutch fan.