What grit paper are you trying to use to knock it flat. If you start with to fine of a grit it will just float over the highs and lows. I'd put a thin skim coat over the thing,water your bondo down with some Plastik Honey or use the thinner fillers like Rage Extreme. Start with 36 grit to get most of the filler off then go to 80 to get it the rest of the way. Make Xs with a long board and keep fresh paper on the thing, don't ride the paper throw it away when it gets dull. Also the better fillers sand easier and save money on paper. After you get done with the filler work you can spray 3 fat coats of Slicksand on it for some good build to help out with getting it flat but be sure and seal it with something before paint. It's a polyester primer and you're not suppose to paint straight over any type of body filler. I'd block the Slicksand with 80 first then get it to 180 and spray some 2k over that and finish with 600 wet for a metallic or 400 if you're gonna use a sealer or it's a solid color. I can't figure out what you used the heat gun for. Chemical stripper will get anything off it you give a little time to work. You can cover it with plastic to keep it wet in hot weather. If it's really worped you might be better off to find another hood, rust usually isn't an issue above the middle of the car. Good luck with it. Bodywork takes a lot of patience, at least good bodywork does.
