Just adding a bit of clarity here. Any box from 1999-2010 will work and have the same wheel well contour as your OEM stock fender. 2011-2016 beds will bolt right on too but the wheel well contour changes. That's where knowing what your long term plan matters.
Here's my 2001 F350. I knew this was going to be my last truck having tried a # of newer 08+ F350/F450s. Newer trucks look nice but are crap, can't work on them and just not worth $100k+. So I went the other route, invested a little money and am as happy as can be.
As you can see nothing about this truck is stock. It even has 08+ rear leaf packs (8" longer) to fix the rear bounce all the 99-07 truck owners have (Mfg rear suspension design defect). Even got the 08+ style Full Power Telescoping/Extending mirrors full operational.
Relatively speaking, yea I have some $ in it. But nothing near the investment compared to new.
This truck (7.3L) is the most reliable. #NoRegret
Going to do the same to my 2005 Ex. Not as happy with this 6.0L but I spent the time to work out all the internal issues, body is next (investment is worth it for me, just can't get anything comparable anymore). I needed something for towing and to tote the grandkids around in.....LOL.
Hope that helps you make some decisions...