Hi Jenny,

I would say check the most obvious factors first and experiment with food choices and adequate hydration.  Think about a belt to carry fluids with you and look into a neck cooling wrap (the kind with the gel or thermafreeze).  They really assist in warmer weather.  Electrolyte and circulation problems can cause severe headaches, for example.  Also, consider any side-effects from medications and the timing of exercise in connection with those.  In other words, is there a way to run at an earlier or later hour to see if that makes a difference and/or a way to alter any other routines?  If you can indentify the contributing influences, then I think you will be fine with positive results.   

Hope you are feeling better and back on the route soon!