I installed the Thule system and it works great. I have a Thule Cascade carrier and it's pretty long. The factory rails wouldn't work because (1) the space is fixed and I couldn't get the proper spacing and still open the tailgate, (2) the carrier wouldn't fit over the antenna. With the Thule system, the antenna is not a problem and I can still open the tailgate fully. The Aero bars a a little more aerodynamic but I can still hear a little wind noise.
Ford part number A7FCS-45053R-AA which is a complete front/rear Thule kit that consists of Thule 450R feet, 53in Aero bars, and lock set for only $256)
http://cgi.ebay.com/ebaymotors/ws/eBayISAPI.dll?ViewItem&item=180474084991
[Just notice the price went up since I bought it)