We successfully modified the hood to make the gaps acceptable. By drilling out a few spot welds where the outer skin attaches to the rear brace, the outer skin easily moves. You can see that we pulled it out almost an inch. Then we bent the flange on the brace outwards to make contact with the skin and welded it back.
I also decided to sand down the bedsides and reclear. Too many imperfections that would need to be sanded and buffed. And a couple spots were on edges so I just sanded it down and will spray 3 more coats.