I would start by getting rid of the intake manifold and putting on a Mopar M1 intake. It not only gives you an increase in HP and torque. (small, but it's there) it also eleminates the problem of a leaking intake belly pan. Which is a very common problem on the 5.9.
Here's a thread about it. http://www.durangoforumz.com/showthread.php?t=28
I've also put a 3 inch body lift on mine and 31 inch tires. I had a flowmaster turbo exhaust installed as well. I wanted to go dual but dodge chose to notch the rear bumper only on one side. It wouldn't have looked right.
MTX makes a sub enclosure that fits in the under floor compartment in the rear hatch. I can't rememnber who made it but there used to be a sub enclosure that replaced the middle seat in the middle row. It looked like a seat but it held a downward facing 10" sub. And you can fit a pretty good sized amp under the middle folding seats as well.