I had a 01 Silver GT and I had the same problem. I took it to the ford dealer 4 times.
1st time they basically told me I was on crack, because it didn't make any noise when the machanic drove it.
2nd time they said they replaced the TOB. They also basically said I didn't know how to drive and that I was riding the clutch.
3rd time was about 50 miles later, they replaced the TOB, clutch cable.
4th time about 100 miles later,
highly pissed this time. I called the 1-800 corprate headquarters and talked to a customer service rep and told them all the problems I was having and if they didn't fix it this time, I was gonna file paper work under the Florida lemon law. That really got them hopping. The Service Manager called me at home about 40 minutes later saying they wanted to do whatever I wanted to make me happy. So they replaced the Clutch, Pressure plate, flywheel, TOB, TOB retainer and clutch cable. They asked me if I wanted a new transmission put in. I declined to have a new transmission put in.
Well about 5000 miles later it happened again.
Well a buddy at a speed shop suggested I try an aftermarket clutch cable. He said the stock cables were crap. If it didn't work, we would install the old one and I could take it back to the dealer. So instead of taking it back, I went and bought a Steeda Firewall clutch adjuster, and adjustable clutch cable. We installed it on a saturday, and I didn't have any other problem for the remaining 60,000 miles I had the car. That a pain in the arse.
Oh and all that happened with the following mods. Subframe connectors, C&L mass air meter, 70mm TB, under-drive pulleys, bassani X-pipe,
Magnaflow cat-back, MIL eliminators, lowered 1 1/2 inches with Tokico adjustable shocks and struts. They didn't say anything about warranty problems even after I call the ford 1-800 number.
Bottom line: call the 1-800 number, have it fixed again at the dealer, then install an aftermarket firewall adjuster and cable. problem gone. My .02.