There is so much stuff for the pre-eagle trucks lol. So your list so far:
CAI - noise, not much else
Catback - also noise, not much else
Tuner - best thing you've done so far
The long tubes won't hurt, though that's going to be custom Y pipe/mid pipe. Between the headers, EGR and possibly messing with cats you may or may not be able to find a tuner willing to do a custom tune (that alters emissions equipment in any way) due to the recent EPA crackdowns. Long tubes generally do not have EGR provision which guess what, your engine has.
A cam swap would do wonders (if you're willing to give up MDS), these engines are woefully undercammed stock. Reason is they can make sufficient power without going overboard and still meet fuel economy goals because of the cylinder heads.
ProCharger makes a bolt in kit for that truck.
Gears
The design of the engine block and the accessory drive is what makes it difficult to use later intake manifolds or even the few aftermarket ones.
The weak link of the 3rd gen is the 545RFE trans. Mild power probably ok. Too far into the 400 hp range and you start living on borrowed time.