i have the same truck as you, see my sig for mods. Yes you can just replace the muffler with a flowmaster. As far as which flowmaster you want is up to you. I personally have the delta flow and love it.
The original 40 series is louder and will create alot of drone in your interior. If you don't mind really hearing your exhaust inside the cab and want to be noticed, then the original 40 series if for you.
The delta flow on the other hand is somewhat quieter and will not create as much interior drone. With mine, it's clearly not stock but it's not annoying. I like the sound it produces at the right volume. My tailpipe is stock in stock location.
Now for the intake, i have the K&N CAI. It didn't do much in the way of performance but you gotta love the sound lol! Makes a nice growl when you get on it on the highway and a nice whoosh sound when you rev it up from a stand still.
The air intake mod is you basically remove the air silencer in your stock air box that houses the air filter. This allows for more flow into the engine. Here check this article out as it should point you in the right direction if you choose to do the airbox mod.
As far as other mods you can do. You can do ignition upgrades such as NGK plugs and wires of your choice. Underdog makes good wires and is a site sponsor here. He's a good one to deal with.
Next thing you can do is an electric fan from jusnes modified. I don't have one due to cost issues for me so i can't say anything personal about it. It is a 16" fan that you install in place of your stock mechanical fan. The efan will remove the drag on your engine that the mechanical fan is producing. Word on this, more power, better cooling and a smoother running engine and better MPG's due to the less drag. Check out www.jusnesmodified.com
for the efan. Runs about $159.
That's all i can think of as far simple bolt on mods go for the 2.5 Everything else is pretty much custom work from there on. Good luck -Mike-