Probably not the answer you want to hear, but the only way you can know for sure is to try cutting wheat out COMPLETELY for *at least* a few weeks to a month. If the headaches go away, you should go for an allergy test, or whatever is they do to see if you have a wheat allergy/intollerance. (Since, that is, headaches is not really a standard IBS symptom). But if you're still getting the headaches after being off wheat for an siginficant amount of time, you should be looking elsewhere for problems (see your doc).
It's also possible that you have a GI yeast overgrowth - headaches can be a symptom of this - so if you don't want to give up wheat totally at first you could try giving up yeast (and sugar) - that does, admittedly, mean lots of wheat things, like bread - but you can buy yeast-free bread. (NOTE: If you want to try that, be sure to google a candida diet or something like that to find out how to completely get off yeast and yeast-supporting foods (i.e. I'm pretty sure anything fermented, vinegar, mushrooms etc. would be out too) - I don't claim to be an expert on this! ).
Anyway, hope that's helpful to you.
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