The 2004-2008 F-150 truck was introduced in January 2003 for the 2004 model year as the redesigned eleventh generation of the F-150 lineup. For the 2006 model year, several improvements were added to the F-150 lineup.
Here' are some images from the 2006 Ford F-150 repair manual, showing the location of the Powertrain Control Module (PCM) in the engine bay for 3 of the engines that can be used in the model.
(click on image and then, when it opens click on the image again to further enlarge)