OK, so I clamped a board with some pennies in the center to crown the frame halves more. As this also caused the skin to rise higher on top than the front skin, I removed some of the spacers I had made. When a couple hours of work finally got the alignment I wanted, I back drilled a flat metal plate, then used that as a template for the holes in the new bracket (which would have covered the holes I needed to use to realign). I then clecoed, double checked everything, and riveted the bracket. NOW, the frame has a much better alignment.
Sacrificial plate clecoed behind so I could backdrill using existing holes in frame
