Have you at least had an MRI to be certain it is not from a disc issue or a circulatory issue of one of the brain arteries?

Does the pain seem to get worse between doses of Mestinon (if you are on it)?

Muscular pain, as these guys have said, can occur when muscles get weaker or are overused.

Have you ever had your heart checked out? What about a sleep study. If you have apnea, it can cause a headache too.

I hope it's "just" the MG and not something else.

Annie