Knock on the sheet metal with your knuckles; it looks like that metal is probably pretty damn stiff in that area, and you may be able to get away with just sealing and fastening a top onto the tire well. I'm not sure I'd even bother fiberglassing that whole thing, it looks stout in there. That fiberglass job in the pictures isn't doing anything except sealing the box anyway, that's barely any fiberglass at all.
I'd say see how stiff the metal is, think about making some shim strips to level out that back edge, then seal and mount a top onto it. That's the easiest way to go unless the sheet metal is flimsy enough to be resonant.