Couple of my opinions:
-Maybe completely eliminate dairy and red meat for a couple weeks to see if there is improvement by reintroducing them and monitoring effects. These don't have to be done all at once just consider these common "intolerances" that could otherwise go unnoticed and wreak havoc.
-Maybe stick with a higher protein (as opposed to vege/fruit/grain), whole food (no sugar--or fake sugar--sauces) based diet. Like hard boiled eggs or natural nut butters without hydrogenated oils--identify and always avoid transfats. Avoid refined, white flours and maybe substitute breads/pastas for sprouted grains when grains must be eaten.
-Do eat plenty of good fats. Use extra virgin coconut oil for cooking and for lower temps e.v. olive oil. Avocados, walnuts, fish oil, flax and real grass fed butter are really good.
-Find 100% vege/fruit juices--no sugar--like bolthouse farms or naked etc. I think carrot juice helps, as does the "green goodness" bolthouse drink.
-Do eat good fibers with prebiotics like steamed broccoli or plantain recipes or apples or squashes.
-Find a quality probiotic supplement that noticeably ameliorates stools and take enteric coated fish oils.
-Stay super hydrated.
Nourishing Traditions is an interesting book for recipes. The author (Jordan Rubin--I agree with many of his opinions and some of his products, like Primal Defense Ultra) of The Makers Diet has good recipes in the back of all his books, probably online too. Whole foods has a good app to cook with real food. See my rantings and pointers at the Success Stories section: "MY Supps for MY Dis-ease".