Yeah, it looks in the picture that you have a tighter bed to cabin gap at the top of the bed, is that accurate?
The door gaps look good front and rear, and the front fender seems to line up with the door nicely, so far as the bodylines.
Honestly it could be a handful of different things going on, most notably age and rust, but I'm having trouble thinking of why the bed would be that far above the actual body, it should be much closer. Even after sustaining a hard hit in the rear, you'd have a better fitment, and typically you'd have other issues.
You're certain that the bed that is currently on your truck, always was with that truck? It wasn't swapped out in the past? Because I'm thinking that someone might have raised the bed for some reason, clearance for tires or something?