Bleached out antler help!

I have a skull that was brought to me to whiten the skull, and stain the faded horns. The skull was left in a pond for about a year to "clean" it. Well when I got it the horns were bleached out white. No problem to stain, but as I looked at it I noticed what looks like blackish mold spots all over it. I have tried to get them off but they are set in pretty good, sand paper won;t get them completely off.
I would like some suggestions on how to get them clean so I can stain them. I thought of maybe using peroxide to completely whiten them, But I haven't this before, so any suggestions would be appreciated!
Some pictures below, not real clear but you may get the idea.

Thanks,
Michael