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I think you just have to keep going (polishing) until they're gone
When I stripped my aluminum valve covers on my 92 they were pitted bad
I sanded and sanded and put on two coats of paint and they looked even worse - then had to put them back on the car because of time constraints so they're on right now looking like crap. The whole engine is coming out next week so it's not an issue I'm just going to throw on LT4 composite covers...
Start with a coarse Al Oxide paper, wet, on a sanding block. Progress through finer grades of paper, each time removing scratches and pits from prior sanding. Finish off with some Al polish. Keeping the paper wet and clean will minimize pitting.
I did the job on the top of the plenum in my IROC and it took some time to get that mirror finish, but it is possible.
Do realize that plenums are different. You might try polishing a couple and see which one you like best and sell the other. Some pits can require a remarkable amount of grinding, sanding, polishing.