Unfortunately I am not near my pickup, so I cannot get any pictures to show the detail you are chasing. I do have some pictures which could help, but I am unable to upload pics at the moment.
The gap you have shown in your pictures does not look correct to me. It appears that either your door is not sitting horizontal, or the panel above the door is sitting up high at the back of the cab. The top of the door should be parallel with the holes that run across the top panel. (I hope that makes sense)
If nothing else, hopefully this bumps your thread and someone else will add some pictures or offer their opinion. Good luck.