My son (10 yo, swcah) has been getting a lot of headaches lately, too.  We think his are mostly sinus related.  Sometimes he complains about his stomach at the same time.  He has even thrown up a couple times - and then is fine.  We figure the drainage is upsetting his stomach - once he gets it out, the belly is ok.

My husband used to get headaches a lot as a kid when playing outside - most likely mild dehydration, so his first question is always "Did you drink any water today?" 

I get migraines, so I also look for triggers, but have not found any with our son.  Chocolate is a trigger for some.  Mine are mostly menstrual related, but I have also found that red wine and Pepsi products are problems (no problem with Coke products, though).

Good luck in determining the problem.  It is frustrating not knowing!