There are probably a half-dozen manufacturers making early Mustang fenders. Some are pretty good, but most are pretty bad. My right fender fit fine, with virtually NO bodywork necessary. My left fender, on the other hand required more than 10 hours of bodywork to get it to line up. The gap between the trailing edge of the fender and the leading edge of the door on that side was terrible. My bodyman was baffled, since the other side went right on. He messed with it and messed with it, even putting a new skin on the door, without any luck.
Finally, it occurred to him that the fender might be grossly mis-stamped, so he took a few measurements and found out that the trailing edge of the fender was off about 1/4" between the top and the bottom. He's put plenty of fenders on old cars over the years and never seen one with just one grossly-bad dimension like this. Usually, if they are bad in one dimension, they are bad in others, too.
Since the rest of the fender fit perfectly,he was reluctant to swap it for another repro that might be even worse. He welded on more metal on the trailing edge and then ground it down 'til it lined up perfectly with the front edge of the door from top to bottom. You'd never know the fender had major surgery, but there is a lesson here:
If your factory fenders are in reasonably good shape (I.E., just typical rust hole at the bottom), repair and recycle them.
Nothing fits better than a 35-year old piece of Ford sheetmetal.