These are good tips here. You say you eat whole wheat. Do you also eat soy? Most soy is genetically-modified and filled with pesticides. These pesticides destroy the lining of your gut and kill off healthy bacteria.
I would suggest three things:
1) Remove all wheat/gluten from your diet for 6-8 weeks
2) Consume only non-GMO organic soy (fermented is best)
3) Add a high-potency probiotic to your diet or start making your own milk kefir or kombucha
Once you rule out gluten intolerance and get your healthy gut bacteria levels up again, you should notice a positive difference.