have you seen any evidence that side of the truck has been in an accident? with the top of the opening fitting well I'd think either the back post is mis-shapen, the front has been pushed in or the door is malformed .... does the feature line on the middle of the door match the cab line as well as the top molding does in pict1? does the front edge fit well all the way down? [really need a fender on to see - should be just slightly inboard of the pillar and fender] ... have you done any work on the step?
if the whole front edge fits well [with the fender on] you may need to bend the door above the feature line, if it fits well at top but is way out at the bottom .... with the front fitting that well [if it does all the way down] I can't see bending hinges helping anything - but still, you need to install the latch and see if that changes alignment any
Bill
The step is a replacement, the line of the door along the step is even. The cab corners were replaced. I had that thought too, but the separation starts higher up than the corner replacement. I found no creased panels, i.e. no evidence of accident or other foul play, just rust and it was Texas truck.