HBarlow is correct. . The stock intake is good for approx 450 rwhp, and stock exhaust is good for over 600 rwhp. There are some reasons to mod the intake/exhuast, but it really does nothing in the total power or economy catergory.
A CAI on a 06 with less than 450 rwhp is a waste of money. If you tow often, or want a little quicker throttle responce then do the following to the intake.
1) A
Home Depot CAI will bring more ambient air into the stock box when boosting hard, this will redice the IAT's and reduce the restriction allowing more, smoother flow.
2) A
Airaid MIT will remove the intake baffles from the tube between the filter and the turbo. This mod direct air into the lower elbow and promotes smooth airflow. This will increase low boost throttle responce, and increase turbo spool. It also makes the turbo a little louder, but still passes the wife test. The best part about the MIT on your 06 is that it leaves the OEM lower elbow in place. The lower elbow has directional vanes that smooth the air as it makes the final 90* turn into the turbo. Holset claims this makes the turbo up to 30% more efficient. There is no aftermarket CAI I know of that does this, right off the bat you have lost performance there with a CAI. This is a low-mid range rpm mod.
3) The OEM intake horn is very restricive. It was built with ease of assembly in mind, not performance. A
GDP Horn is the best bang for the buck on the intake horns, and it will hold a MK2+ filter kit if you want one. But the intake horn will decrease low end smoke (if you run a tuner), increase throttle responce, and increase turbo spool. I also saw 2-3* lower IAT's with the horn than pre-horn. This is a low-mid range rpm mod.
As for air filters, the OEM is the best on the market now. Be sure it has the OEM 4" pleat version.
Also, if you don't have service records for the truck I would start with a full fluid change, to include power steering and brake fluid. This will get you back to square one. I also highly suggest additional fuel filtration, such as the
GDP MK2+ kit.
If you want a little extra power consider a Smarty Jr. You didn't say if it was a manual or an auto, but if its an auto I wouldn't go above SW1 until you can finance a tq converter and a valve body. But SW1 will give you a small bump in economy and a nice boost in mid range power.
As for your warranty, anything can potentially void it. The Smarty Jr isn't traceable when returned to stock, so they can't void an unrelated item based on the tuner. Your warranty expires 5 years from the in-service date. You should be able to call any Dodge dealership, give them your VIN, and find out what warranty you have left.