I've been working with badly pitted sheetmetal. I alternately spray the surface with a phosphoric acid solution and then use a wire brush attachment in a small grinder to clean the pits. The process is slow and laborous if you want the pits absolutely clean.
I have also used a suction sand blaster with good results using copper slag. Of course, you have to be careful as even the low pressure sand blasting is heating and removing metal.
Another alternative is to use the phosphoric acid and wire brush to remove the loose rust and convert the remaining pits. Apply a moisture cured urethane primer. Sand the surface allowing the urethane primer to remain in the pits. Spray epoxy primer over all.
