hello Anthony, If all else is good at other areas of the car then my first thought would be that the problem is localized at that right door and fender. But...you must make sure your fram is not bowed. Then again if your left door is not a problem then if it is the frame it might be atributable to something like a hard jolt to the right rear portion of the car which might have tweaked just the right rear frame. So check that stuff over real good.
Here is something I would tend to believe. If the frame has bowed because of the classic situation whereby the rear axle was pounding on its snubber pads a few too many times,... Then I believe the gap at the top area of the door to rear fender joint would be closed up alot. You do see this on some cars where the gap is closed up enough to chip the paint, etc. BUT!! If this is the mechanism of force that occured, I don't believe the fender would be pushed up higher. At least not by much. Just the gap would be closed up. To push the fender higher, you would need a force applied vertically almost right below where it is higher. Maybe in a situation where you ran off the road and landed on the crown of a ditch or on a large rock. So If neither of these mechanisms of force appear to have occured, I suspect that there is just pieces not mounted correctly. Make sure that there has not been some previous metal and body work that was aligned poorly. One such component that comes to mind is the rocker panel. After I had done some considerable work on my car, including a new latch pillar and near completion of the rear fender, i went to install the rocker panel and realized that I had put the latch pillar in too low. Here is the sequence of events that I believe at this point is the best way to get things where they belong. Hang the door, then the front fender, then match them exactly as you believe they belong. then the rocker, next the latch pillar and finally the rear fender. In your case, if everything is solid, and you find nothing else wrong, then I would try to gently hammer and dolly the door curviture to match the fender. Just open up the radius of the door curve alittle to raise the top edge.
---- Oh, one more point, make sure that the fender is not mounted too high on the shroud. And could the fender be tilted just alittle with its front upper most point tilted up.
Cheers.