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does a comma go before as well as?

This is a 38-year-old female with a past medical history of degenerative disease of the cervical spine as well as migraine, who presents for her annual physical. 
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You are correct with no comma before "as well as".  You could clean up the sentence and eliminate a few unnecessary words, where it could read as:
"This is a 38 year old female presenting for her annual physical. Her medical history includes cervical spine degenerative disease and migraine."
Saying "past medical history" is redundant, where "medical history" means the same thing. I hope that is helpful.
No, because it is an essential relative clause. Only non-essential relative clauses need to be offset by commas.