I used to have a 96 Jeep Grand Cherokee Limited with the 5.2L engine (318 Magnum) that I installed a set of high quality Mike Leach headers specifically designed for this application; the K&N fuel injection performance kit (cold air filter); Mopar performance computer; larger injectors; larger throttle body; 3 inch stainless steel exhaust front to rear (not just cat back); high flow cat; high flow muffler (still pretty loud); and a few other mods. After about a year I started wishing I could meet somebody that had a factory stock Jeep that would trade me straight across. I really hated the way it drove. I got rid of it and bought my 06 F150 with 5.4L. I bought an Edge tuner thinking it would help with towing and fuel mileage. I could definitely tell a difference, but it wasn't an improvement. My truck ran better and towed better without the tuner. I returned to truck to stock and sold the tuner and am much happier for it.
I've come to the conclusion that, as much as we may like to think otherwise, those guys in Detroit have a pretty good handle on what it takes to build a truck that meets the needs of the majority of the population with a good degree of drive ability and reliability. If you look around, just about every "old" truck you see on the road is bone stock and simply properly maintained. All the "improved" trucks can be found in the junkyard or on shyster used car lots.
Leave your truck stock and don't overload it. Take good care of it and put all that "upgrade" money in your pocket.