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If you trace it out with wiring diagrams, then keep in mind that Ford made a major wiring change in model year 2002.
The wiring between 99 and 2001 is closely the same, but wiring from 2002 up is different. Ford made a very big deal about informing the body builder and upfitter community about this change back in the summer of 2001, for the upcoming 2002 model year.
So Tugly's recommendation to get both 2000 and 2005 model year wiring diagrams is spot on. Ford DID make changes. I don't know what all the changes were, and if they relate to what you are experiencing, but the differences in wiring colors and components was quite evident on the trucks I've worked on.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.