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Decent beds for the 1999-2016 trucks are getting harder and harder to find, especially short beds. I see them online for $2500-$5000+. If you can find a good one and score a good deal on it, that is the easiest path forward, but it will be expensive.
A lot of companies make patch panels and replacement supports for the beds. LMC trucks comes to mind, but don't consider that an endorsement. I've never used their body panels.
Also, before you ask, yes, an aluminum bed from a 2017+ truck can be made to fit, but the body lines don't match at all. Calling it "goofy looking" is being kind.
Check out Keith's Truck Service 814-696-6008 in Duncansville Pa. out by State College Pa. He had about 100 beds 3 years ago in Red Silver and White. Picked up a 2015 8 food bed with lights and tailgate for my 2003 Super Duty for $3100.00. These are take off beds brand new.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.