Your grades are, as pointed out above, weak. But what about your research? It seems you are really passionate about it. Why don't you get a job at a research institution, try to shine by your hard work and passion, and reapply? I know this will take many years and energy. But if you are truly passionate, you may pull this. If this is too risky, why not take math classes at a good school nearby you for a couple years? If you dedicate a couple years to math courses, you may be able to squeeze grad real analysis in. That will help your profile a lot. Either way, it will be quite time consuming to make up.