I would be inclined to use the tools out there that weld a stud to the sheet metal and pull out deep dents or low spots with a slide hammer.
Lead probably would work better than fillers like bondo but be very sure you are aware of the dangers of lead fumes. OSHA has regulations covering lead exposure which I would read. At one foundry I was familiar with, the guys exposed to lead fumes would work for 15 minutes and then get away from that area I believe for and hour. As far as suitability for the intended purpose I think the lead will work certainly better than Bondo. Just be sure to be careful of your health while working with it.