Birchwood Casey makes a product called Aluminum Black. I dont know if you will be able to make the spots disappear, but it will make them much less noticeable.
Keep in mind, you will possibly lower the value by trying to restore the finish. There are collectors who value the original finish, blotches included.
The new 638 is marked .38 +P, so I would be hesitant to fire +P loads in a vintage Model 38.