How old is your daughter?
Depending on how old she is, could it be a result of puberty?
Do you remember if she have a sore throat, or swollen lymph nodes in her neck when it all started? Has she been tested for mono?
Those are the first two things that popped into my head when I read your post. I had stomach aches and headaches and random fits of fatigue when I had mono, and it lasted more than a year. Mine started off with a sore throat and swollen nodes, but I know of others who had mono and didn't get that. It could be worth looking into.
In the meantime, fresh ginger root tea is a great remedy for stomach pains, and headaches (and a whole list of other things), and can help strengthen the immune system to fight off whatever is ailing her. It doesn't taste awesome, but add a little honey and tell her to swallow it down fast.