So are you talking about the distance the inner pannel sticks out past your newly installed patch at the pinch weld? Well the patch is rusted pretty badly there too. And as far as a perfect match, in an area like that on any car or truck would be impossible. The factory guys could have trimed to fit in that area as well during assembly, sheet metal forming is still not an exact manufacturing process, especially on something like a car or truck body.
Even the reproduction outfits like dynacorn say its not a perfect fit for everything. And probably a good idea to mock up before painting it all. Yours too, put the windshield in to test everything, I would.
http://www.dynacornclassicbodies.com/classic2.html