Since finishing my re-wiring over the summer, I have been spending most of my time on body work, and got a nice driver side fender for my car, (finally, it's the second one I bought) it fit and alligned nice except in one spot, the door.
My first thought was to blame the fender, since it is an aftermarket, however while looking at the passenger side I noticed it's door was mounted higher than the driver side and it alligns nicely.
the door is the original and has never been off the car, but it sits lower than the fender by less than 1/4 of an inch, the door just looks to be mounted too low.
I tried a GM fender as well and it has the same issue. I threw in a photo to help illustrate what it looks like. sorry, it's not a very good one, you can't really see it but the lower door crease is sitting below the one on the fender!
any thoughts on how to correct this? for any suggestions.

 

i have a similar problem, my door sits about the same gap as yours does away from the fender at the top, i havent really looked at it too much but i have a hunch its the top set of bushings/pin. does the door/fender "pop" when its opened?

 

Door/Fenders are probably the worst thing to ajust on these cars. Took me about 10 hours to do it on both side of my car. The best tip... Dont be afraid to bust out the die grinder and enlarge the mounting holes where the fender meets the rocker panels, and add shims (washers can do) under your fenders/doors bolts to place them in their perfect position.

You need to slack all the bolts holding the fenders, I mean, all of them and start getting the fender alligned from the door, to the nose. Start by the top of the fender, where you have the big gap in your pic, then work your way all the way down to the rocker panel. Then tight the bolts from the back of the fender to the nose. Heres a pic showing the gaps after tons of hours of fun.

Hope this help.

 

It could also be door sag. A common problem on these cars. Check out Top Down Solutions for a hinge repair kit, and door aligner.