My 01 was doing the exact same thing about a year ago, and still is. I've had it to the dealership 6 times for the noise.. 1st time, they lubed the break pedal shaft. That worked for about 3 days! 2nd time, they replaced the Hydro Booster... No luck.. 3rd time, the tech said he couldn't hear it.. Loud one day, quiet the next!?!?!?! Waited till it was loud again, 4th trip they ordered a new break assembley. Replaced on the 5th trip, still no luck! 6th trip, they told me it was a trait on these trucks.. Pretty much telling me I had to deal with it. I asked him why the heck they replace a $700 Hydro Booster and $200 Break Assembley if it's a trait?? Then told him to show me one of these new trucks on the lot, I wanted to see if they were making the same noise. Instead of a new truck, the service manager took me to his truck, which was an 04 F250 and he couldn't get it to make not one peep. Then he took me over to another truck they were working on, looked like an older model like mine and it made a slight noise, but nothing like the "Frogger getting run over" sound mine was making. He appologized and told me that the hydro booster bushings may need to be broken in before it quits.. Well, it hasn't quit yet and I'm sure the bushings are broke in well by now..
Pretty much the only thing they did that halfway worked for a little while, was the lube job on break pedal shaft. Everything else was pretty much just throwing parts at it. Only thing they didn't replace was the master cyl. Maybe that's the culprit, but I doubt it. Hope this helps you guys out.. Let me know if ya'll find out anything on this..
Thanks