Thanks guys.
For the remaining holes that are there, I think I'm going to put another piece of metal behind them, to use to build the blobs up. No-one will see the inside piece, and it will help to keep me from burning those holes any bigger. I don't want to have to use a bunch of Bondo there, and I don't want to eat up any more original metal.
Now if it would just stop raining! It's 5/29 and it's 40 degrees out!!