You may have already looked at it, but for what it's worth-
A few issues to look for aside form the other nickle and dime things on a 13 year old truck:
Not sure where you are at, but I'd check the rockers behind the running boards for rust, as well as the seam on the top of the rocker that you can see when the rear door is open.
AWD- check the transfer case for any noises (drive slow- idle speed with your foot off the brake) with your door open to listen for any "popping" noises.
Check the driveshaft u-joints underneath for any movement.
Check the exhaust manifolds for cracks, especially the passenger side. If you have a laser heat gun, that can help out in the process.