If you insist on I have been having... , why not. However, as no action is involved, I would simply say I have had a headache for two days .
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TuongvanYou will often see a lot of such sentences in letters sent to doctors asking about how to treat their illness.many of the letters are written by native speakers. I am sure!I never doubted your sentences weren't written by native speakers. I just mentioned mypreference!