I fixed the problem. If you look in the picture, the bottom two nuts fit in a recessed pocket. The top nut sits on a protrusion in the reinforcement bracket. I used a hole saw that piloted on the outside of the protrusion, flipped it over and welded it back onto the bracket. This allows the top nut to be recessed, like the bottom nuts. I used a 6mm flat washer and nut, which is shorter than the gold nut n the picture. Then, I cut the stud flush with the top of the nut. The door panel now fits.