Can symptoms from the brain eating amoeba come for a few hours and suddenly go away and than come back. and is the headache always severe?

I am not sure why you are so concerned about this very rare disease. Headache and backache are the 2 most common symptoms that a family doctor has to address everyday but the average American doctor has never seen a case of brain eating amoeba in his (her) entire career. This parasite causes severe infection, meningoencephalitis, headache which is severe and persistent is only one of many symptoms

If you are having severe headaches see a neurologist. A spinal tap would be considered if you have signs of meningitis