I assume this filter your talking about is an inline so called "whole house filter". If so, it's doing you no good at all. Just remove the cartridge.
Sounds like you needed an iron filter more than a water softener. Even though 9 grains hard is not considered soft, its not too bad either. .25 ppm of iron will stain though and an iron filter would have removed it. The black is probably sulphur. Does the water have any odor to it?