I replaced the battery in my 2006 f-150 5.4 Liter and now it is running in failsafe mode. What could be wrong?

 

This is just a WAG but after a complete loss of power for a specified time the "keep alive" function of the PCM is lost making the first 10 miles a new learning curve for the PCM, adapative driving Ford calls it. This might be your issue however I'm not familiar with the fail safe mode of the Ford vehicles--I always suggested just rebooting which sometimes takes you out of safe mode (ala Windows XP Pro!)

Hope you have this resolved by now?

 

Thanks for the suggestion JWA after trying everything under the sun including your suggestion to disconnect the battery and reboot I decided to have it towed to the Ford dealer. It turned out it was the Trottle Body Control Assembly. The theory they gave is it was slowly going bad but the PCM compensated for it. After the battery was disconnected and reconnected the PCM returned to Basic operating Mode and it was too much to overcome at that point.

Thanks Again,
Little Beaver