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Welcom to the site. You will have to go aftermarket. Ford did not start selling trailer brake controllers until the 2005 model. I believe the most popular controller around here is the Tekonsha Prodigy, although I think they have a newer model that is becoming very popular also. Just be sure to get the Ford plug in adapter and you won't have to do any wiring at all, there is already a plug wired in behind your dash that the controller will plug into.
If you scroll down a ways on the main forum page you will see a towing/trailer forum. Those guys can probably answer any question you will ever have about trailers/brakes/controllers/etc.
Actually wlihntr, I'm not so sure you can at least not without a major overhaul. The trialer brake controller is wired into the PCM and ABS systems, so he would have to switch all of that stuff too. Not to mention he has the 7.3L diesel, which means the PCM from the 2005+ 6.0L deisel would take a lot of custom work to get it going, if it is even possible. Then he has a different transmission than the 05-07 trucks so that is another major issue, etc
I think you may be thinking of adding the 05-07 upfitter switches to a 99-04 truck. That can be done with a bit of work.
FYI - I got my Prodigy last summer for $70. etrailer.com had a good price and Tekonsha was offering a $20 mail in rebate from their website. Not bragging, just thought I'd give you a benchmark so you know how much to pay.
I just bought a Prodigy as well. Best deal I could find was a guy on ebay sells them brand new along with your specific cable for $111 with free shipping. Bought it Wed eve and got it UPS on Friday.
The best deal otherwise was some place online... $94 + ~$12 (cable) + shipping which exceeded $111.