Looks like you have a 1/4" gap between the door and rear quarter on yours too. I heard the goodmark ones dont fit super perfect, i like your idea of bringing the cut down to preserve the upper lines.
A few questions.
1 did you butt weld the panels or flange weld them with joggle and an overlap?
2 did you use the whole goodmark panel where it meets the valance, or did you cut it there too and seam it back with the stock panel?
3 how far back from the original panels edge did you go at the front by the door and the top? It looks like 1" back from the pic.