If its just the CAI or off-roads you can get away with the strategy tunes that come on some handheld programmers or a download from reputable sources (i.e., Steeda, Brenspeed, etc.)
If your looking to build on what you have and continue with more advanced mods (i.e., cams, bigger TB, power-adders, etc.) that require re-tuning, then make the connections locally on "who tunes" Fords (preferably with a dyno) so you can update and re-tune as necessary. Obviously, more expensive, but your chances of getting done right are much better.