To add to the above, the early V8 6 speeds suffered from a shift bump issue when shifting between 1st and 2nd which required a re-flash from the dealer, although I would assume at this point most out there have been re-flashed. Other than that the 6 Speed is a far more robust transmission and isn't prone to the same issues as the 5spd.
Few other issues with these years....
2006-2007's V8's are notorious for having issues with exhaust manifold leaks, the studs are weak and after hundreds of heat cycles often break and the manifolds also warp or crack themselves, which will result in a small leak and a "ticking" sound until the engine warms. Both sides had broken studs and cracked manifolds on my 2007, luckily I bought an extended warranty and had the dealer do them.
2006-2007 (V8 only) also have known issues with carbon buildup around the base of the plugs (as most ford 3V V8's) which can lead to getting stuck in the head which will require special removal tools.
Can have radiator issues, mostly the early V6's, but even early V8's, mine blew at 70k miles (top plastic tank cracked), it took around 150k to kill the one in my '91 Ex....
Front wheel bearing hub assemblys can wear pretty rapidly, did mine at about 65K and it from the looks of it when i took it apart this would be its third set. Hopefully the Moog's I put in last far longer.
Being a heavy body on frame SUV, sway bar links and other suspensions components often need replacing. In about 30K I've already replaced all 4 links, and the front sway bar bushings to the frame twice. Also had lower ball joints done at about 75K too.
