Draining sediment out of my hot water heater
One common fix for smelly hot water heated in a conventional tank style water heater is to replace the magnesium type anode rod with an aluminum or zinc made rod.  For some reason the magnesium rod coming into contact with certain water chemistry results in a less than pleasant odor. As to the water quality in your flushing the tank, you are over-thinking it.  Put it back into service. That is not your problem. Areas with severe iron content problems often have to consult with and get help from a professional water quality expert.  It can take very special chemistry to deal with problem chemistry. Good Luck. P.