Low slope roof (2:12) – acceptable for metal roofing

The minimum is typically 2/12 pitch for asphalt shingles, although for low pitch roofs (4/12 or less) there may be a different installation specification depending on the manufacturer. Just make sure you follow the recommended install procedure to maintain warranty coverage (and pick a manufacturer that will be around long enough to honor it). In any case, the underlayment should be doubled. Tabbed shingles would be OK, but my preference would be a high quality architectural shingle.

That said, if it's just a small section of the roof (maybe a square or less) and you're really worried about it, you could always go with a flat roof covering like EPDM. The only consideration with something like that is that it lacks any sort of "street appeal" if the roof deck is in any way visible from the ground.

If you do decide to go with asphalt, I don't see any reason not to use a roofing nailer.

First: yes you need to remove all the rust before repainting, or the paint will just flake off as the rust continues.

Next: you need to make sure that there's some "body" left after initial sanding/scraping of rust, or you might as well replace the sheets. You also need to verify that all rust is on the top, i.e. there's no leaking and bottom-side rust (or you'll need to fix the leaks).

Assuming all that went "ok," then sand & scrape all the loose rust off, and do your best to sand off the rest. Paint all exposed areas (with rust pits or not) with a "rust reducer" paint, available at any hardware store. Typically these go on white and cure black; they both reverse the oxidation (rust turned back into iron) and provide a good surface for painting. Then put down whatever color of metal-compatible paint you want.