A lot of those areas are where steel parts are attached to the bike, so it is probably a galvanic reaction between them. Not necessarily a big deal.

On Trek an Cannondale aluminum of that era, steel forks were the original offering, and then later were the fork for lower end models. You can see this in the catalogs, which are all available online.

Another way to go is to strip the frame with Citrus strip and then polish it with a buffing wheel and stainless polish. But your plan sounds good.