Warranty coverage is always from the in-service date, and corrosion coverage is 5 years/ unlimited miles. I'm assuming this truck was sold new in the summer of 2000? How else could it be "3 months out of warranty?"

Although Ford's warranty excludes damage from salt, I'd fight this tooth and nail. You're right- this damage didn't suddenly occur in the past 3 months, so it had to have been pretty extensive BEFORE the warranty expired. BTW, is the damage visible while standing by the truck? Ford's rust-through coverage is for OUTER body sheet metal; if the rust is on the inside (and you'd have to put it up on a lift or crawl underneath to see it), they may deny you coverage.