The short story is that.for now I am punting, and just sealing with caulk. Here is my thought process. The nails left slight indents, and of course a hole. It might be possible to hammer and dolly them flat, but there would still be a hole. Welding would be the only way to fix that, and that would mean striping some or all of the floor pan and then grinding any weld flat. The original factory appearance would be permanently lost. I am not ready to take that step. I never drive the car in rain, so I'm not really worried about getting water under the carpet, but I wanted to seal the holes anyway.

What would you do under the circumstances?

Dave