Since Janet decided this needed a little 'bump' and no one else is answering, I'll give my advice.

If all the seals are are good, no pool water should ever reach the metal parts - so whatever treatment you use won't effect them!

However, we live in an ~'imperfect' world, so if you have a union in front of the pump -- you can remove the motor and disconnect the housing from the influent line and soak (using muriatic and ascorbic acids for the different problems) the whole housing to rid yourself of the unwanted scale or stains.

If you take the motor off, you may need to replace the 'pump housing gasket'.