Headders and a cat on a 3.9? Hmm... I don't think you are honestly going to get what you want out of that motor. I drove a 3.9 Dodge Dakota once and it had a straight pipe out the passenger side. The sound could be described as more of a "I lost my muffler and I'm such a flamer I think I'll leave it off" than anything. If you are looking for the deep effect you might have to spend WAY more than you would as compared to a V-8 to get that sound (which just needs straight pipes). Just curious, what year? Are you going to go hick style (c'mon be honest) or are you going to have a nice truck? To do any significant lifting with big tires you could be spending 2g or more (tires, axles or different gears, liftkit, new rims). Exaust, depending on how extensive, 50 bucks to 1g. Motor enhancements, such as intake (rice) could cost anywhere from 50 bucks for a K&N to... i don't think theres big aftermarket for 3.9's so... 2g for a 318 crate motor.
So basically what i'm trying to say is a 3.9 is not in my book what will work for what you are trying to do. BUT, if you are just going for a slightly more aggressive appearance, sound and get a little more bite out of the motor, than go for it. You will spend most of your money, i think getting the exaust to sound right... Although a kid in my school put glasspacks on his V-6 Chevy pickup and it sounded fine, but it wasn't nessecarily deep. If you have anymore questions, I might be able to help yet still...