This sounds like a very complex case that requires the input of a good specialty pediatrics team to help sort out what might be going on. Not knowing the specific details of the case, the combination of nightly nausea and headaches is concerning to me, because these symptoms together require ruling out a serious neurological problem, such as a tumor in the brain. Since your daughter has seen a lot of doctors, I suspect that this possibility has already been ruled out but, if not, this would be something to talk to your daughter's neurologist
or primary care doctor
It also sounds like there is room for your neurologist to weigh in on the other symptoms regardless. For example, topamax and phenobarbital are medications that are commonly used for migraine headaches and seizure problems, and it is possible that your daughter's symptoms are related either to need to play around with these medication doses. If the headaches are poorly controlled, the medications may need to be adjusted up; alternatively, nausea and headache can also sometimes be a sign of too high a dose.
I would also followup with your daughter's gastroenterologist
to see if additional lab work or other testing needs to be done to rule out a gastrointestinal component here.