Hi:
As a Integrative Health & Nutrition Coach (here with as a mom with a 14yr old recovering from a traumatic brain injury) I can tell you that food is all about bio-individuality - meaning you have to try each food to see if it works for you. Three weeks with a headache is way too long. There are many other Gluten free options:
Quinoa flour, brown rice flour, buckwheat flour (no it does not contain any gluten). Also, for a quick bagel, try Udi's bagels - they taste just like the real thing and they have cinnamon raisin ones, too (My son is on a gluten free diet because of his TBI and he loves them. They don't look like a hockey puck like some other gluten free bagels.

Hope this helps,
Tina Sullivan
Nourish Your Noggin