Rick, that looks intentional to me. There's a couple spots, the bottom most slice, that look like a sazall or tin snips went after the sheet metal.
I'd cut out the bent in pieces in the tranny hump and using the other side as a form bend up some sheetmetal to weld back in. As for the rest of the floors - you can get partial floor pans. Where are you located? If you're in the Buffalo area I can get you a deal on some Sherman parts through my car club.