OK, I know this is an old thread, but I've seen this in several places and never the right answer. This exact problem happened on my wife's 2002 GT convertible. I found the blown fuse and replaced it, turned on the lights and it blew again! Replaced the headlight switch, and blew the same fuse AGAIN! Now, I realize, I'm stupid. But eventually, if you hit me in the head enough times, I'll duck. So I bought a Ford shop manual and started going through the entire wiring harness looking for the short. The good news is that the wiring harness on these things is really pretty bullet proof. The bad news is that there's only a little bit of crinkle-wrap and a curved piece of plastic preventing you from crimping the tail-light wiring together if you stuff the trunk and slam the lid.
So, after removing the crinkle-wrap from the trunk lid wiring harness and finding a melted mess of copper and PVC inside, I ran to Home Depot and bought a box of butt-splice crimp connectors. After a couple of quality hours spent with the splices, a Klein crimp tool, some NAPA auto-grade heat shrink tubing, and a heat gun, I wrapped the whole thing in new heavy-duty crinkle wrap and some 3M automotive-grade vinyl electrical tape, and called it done.
I then called my wife out to the carport, pointed at the repair, and told her that if she can break it again we have to talk about getting her some anger-management classes.