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Joined: Tue Dec 5th, 2017
Location: Michigan, USA
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Even when new, it's fairly common for the box to be slightly misaligned with the rear window or for the top of the tailgate to be visibly skewed with respect to the top front of the box. Shimming the bed mounting points can improve the appearance but it may take a few tries to make it look its best from all angles.
At higher age/mileage, it is sometimes the cab mounts that are at fault. Rubber could be deteriorated or the cab's metal mounting points could be rusted away.
Also, the bed has some sheet metal cross channels welded to its underside to strengthen the bed floor. In effect, these are "spacers" where the bed bolts pass through them. Check to see if any of those have collapsed from rust.
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2003 FX4 Level II, Supercharged 5.0L V8, Headers, Duals, BW4406 manual T/C
Aussie Locker, Torsen L/S, 4.10's, Bilstein 7100 rezzies, Cadillac/Mustang rear discs, Duff traction bars
Keypad Entry, Lock LEDs, sway bar discos, Heated seats, Explorer EATC, Trip Computer and consoles
Other rides:
2016 C-MAX Energi (plug-in Hybrid)
2011 Taurus SEL (highway cruiser)
2003 Ranger 2.3L M5ODR1 Regular Cab (drudge)