If you are low in iron or you were near low and you clean out your system could it make things worse?

I don't know what you mean by "clean out my system", so I can't address that. Low iron in females is usually related to blood loss during the monthly menstrual cycle. A multiple vitamin with iron may be all you need to combat that. The infection, if it is chronic and may affect multiple tissues other than your hair follicles, could be affecting you. Have you been diagnosed with one of the chronic staph infections? Your symptoms are serious enough that they should be investigated, so I'm glad you are seeing a doctor soon.