The problem is the supercharger. many folks run a crossover with a single exhaust becuase a crawler doesn't have to breathe. It fits better and works well at low RPMs. your truck sounds like it's built for power. A mud bogger, perhaps?
A 40 doesn't have room down the right side to run a pipe without going outside the frame or under the transfer case. Neither is the best option for wheeling it. I have seen them with two pipes running side by side or one on top of the other down the left side. then you could put one out each side for bling, or just dump them both out the left. if your doing mud or sand drags or just pimpin' it on the street, then running outside the frame will work, I guess.
Theres plenty of room under the back if your tank is under the passenger seat. You can run all kinds of stuff back there. The cats would be an issue, but a competant exhaust shop should be able to get them both in the space under the driver's area. They need to be reasonably close to the engine to work. If you want to run cats, then maybe running both pipes down the driver's side, over the axle, then cross over with mufflers behind and parallel to the axle, dumping to the right.
Ram's horns work great on a NA engine. I generally do not like headers, but it seems to be silly to supercharge it and not let the air out.