Tuning is probably gonna be those most advantageous to that thing. Those 5.3's can really be woken up with tuning. The electronic torque management completely retards the motors and would be the very first thing that I would do. EFI Live works wonders on those. You could even get someone to tune it for you.
Or Diablo Sport Predator has an awesome bang for your buck tuner that can work wonders on those, as well as disabling the tq management, tuning, diagnostics, ect.
I wouldnt mess with an exhaust personally. Some of these systems these days flow so well stock, its hard to justify the money for just a couple freed up h.p. And if you're the exhaust kinda guy, then I'd recommend Magnaflow. Its a low, deep, throaty system that dosent crackle or sound anything like the typical run of the mill FlowMasters do. Throw a couple resonators on it and it'll be nearly as quiet as stock but with a deep throaty voice box and the same amount of performance.
I'd block off the resonator on the intake side and maybe get a higher flowing filter from S&B or something like that. Pop the screen out of the MAF and it'll be breathing better.