My daughter started getting some similar symptoms at age 13 & we found it was due to a severe allergy to abything remotely petroleum based - petrol, oil, vaseline, many perfumes, cleansers etc etc etc - we discovered the cause after we bought her an entire bedroom suite of solid wood (they'd used a petroleum based "thing" in finishing it!! It was 6 months before we decontaminated the furniture & she was able to go back into her room).
Recently we weent into a shopping centre & separated to do 2 different things & 10 mins tops later when I got back to the car she was standing banging her head against the window because that was less painful than the ehadache the chemicals I hadn't really even smelt had caused her, not to mention, nausea, rashes, cramps, & itches that make her bite at her skin.
I do think you need to rule out neurological possibilities & also hormonal (at her age any hormonal imbalance no matter how slight may be enough to make things worse even if they don't actually cause them). But don't rule out allergies either.