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Are the headaches so severe that they incapacitate you? Is the pain throbbing? How long do they last? Are they accompanied by nausea? Are they preceded by flashing lights, dizzyness, localized numbness or localized weakness?
Migraine headaches are often so severe that they incapacitate the sufferer for time periods that range from several hours to several days. The pain is often described as unilateral and throbbing, but this varies. In addition to sensitivity to light (photophobia) and sound (phonophobia) they're often accompanied by nausea with or without vomiting. The sufferer may also experience an aura of flashing lights, dizzyness, or even stroke-like symptoms such as unilateral numbness and / or weakness.

Judging from your description I can't really say yet whether you're having migraine headaches or not. The fact that you're having generalized body aches argues that it could be just a virus. It's also possible that you might have migraines that are temporary, having been triggered by the virus. What are you taking for the headache? I would recommend 600 mg of Ibuprofen every 6 hours as needed. Sleep should also help. If the headaches persist until late next week I'd see the doctor again.