I started out using flux-core wire on my truck. I think it was .035" inner shield wire. I had quite a bit of trouble with burn-through on clean, sound bed sides. After switching over to solid wire (.023 or .025, I forget the exact size) and shielding gas (75% argon, 25% CO2), I had no further burn-through problems under the same conditions. Disclaimer: I'm an amateur welder at best!
To actually fill the holes, could you cut a metal disk to just fit in the hole and hold it in place from the front side with a bit of masking tape? Leave one edge uncovered and make your tack weld there. I did several like this in several different situations and had good luck with it.
