If you have a CAI like a K&N you might have some problems getting engine warranty work done.if your wanting to mod in the future. you should wait till after you mod the truck. or else you'll just have to get a new tune again.
but if your gonna keep it stock id say just leave it stock tune. and get a aftermarket CAI that has the box around it to seperate it from the engine bay. that should help out on power along with get a better exhaust system. and you should be good.