Hey mannyrock:
I have encountered this type of problem a few times. I have found that a good polishing, down to the clean metal, and some fine (white) polish on the buffing wheel normally takes care of the problem spots. Then a good blueing in the tanks are required to bring them back to like new condition, not cheap but effective.
If they are not too bad, I have used a pencil(lead/graphite), a regular school pencil or a big carpenters pencil can sometimes remove very superficial flecks. Just use the pencil in the same fashon as you would do if you were trying to cover a writing mistake and had no eraser on your pencil,,,remember when you were in school as a child and you had already chewed the eraser off, made a mistake then scratch it out with the lead, you can rub pretty firmly. Well that's how I use it. Then you can use cold blueing to touch it up, not factory equivalent but a touch up only. NO GUARANTEES, it's just what I do when people don't want to pay for reblueing. Try first on an unseen place which is normally covered/out of sight first, then proceed if satisfied with results. On a nice gun,,,,,,I would opt for a professional job, unless I planned on a lot of field use was in the future for them then the cheaper solution would be acceptable to me.
I agree with Graybeard about the plastic storeage and using only 0000 steel wool for rubbing the blueing. I learned about the plastic storeage on a mark 1 ruger,,pitted with rust that would not clean-up, still shoots good tho.
These only my opinions and experiences, they have worked for me,,,I hope something here helps you.
safety first
HM