Also had this issue since 27k miles when i bought the truck. Most of the time the bending only made the gaps worse and didn't fix the body rub. I then just pulled on the door as i swung it open, esp when perpendicular to the body to get it open w/o the rub. Amazingly, a few days ago as i was doing this at the pump, i heard a "pop/ping" and the door now operates perfectly and lines up better as well! I *think* that bracket that holds the hinge was bent concave and i "popped" it back straight or even convex. I can't be sure since i wasn't really trying to fix it at the time tho, sorry.