Check to be sure the exhaust manifold studs are not broken. Both sides on mine broke. (4.6 V8) and were repaired under warranty, but had they not been under warranty would have probably been about 1k+ each to fix. The problem is the manifolds warp when heating/cooling and breaks the studs off inside the head, which then require them to be drilled out and the manifolds replaced.
Only way to really check for it is start the vehicle up when it is cold (as in sitting overnight) because once the manifold warms up, it seals off the break. It will sound like a ticking or snapping sound at idle or acceleration, and will go away after like 10 or 15 seconds depending on how cold it was.
Had a recall done for the park/shift interlock (was hard to put into gear from park occasionally)
Have had the trans reprogrammed under a TSB for the tranny bump, but it came back a few thousand miles later. I just live with it.
Other than that, I have had no issues with it, and ordered it in early July 2006, delivered to me August 2006 (Got my name on the window sticker even!)