He has several allergies, dairy being the biggest, and I have been dairy free since he was 4 weeks old. I had him tested and I eliminated all of the allergens that he tested positive for for 3 weeks, and saw NO difference in his sleep. I still am dairy free, and I limit the other foods that he tested positive for.
I would suggest heading over to the allergy board. The women on there could give alot of insight on how to start an elimination diet. I would be willing to bet the farm that this is all caused by food issues. Good luck!
ETA: I just went back and skimmed some of the responses. I totally understand that it is hard to eliminate alot of things from your diet, but it can be done. I am currently pg and on a *very* restricted diet because of dd's allergies. Currently we avoid completely dairy, wheat, egg, soy, peanuts, tree nuts, almost all seeds, bananas, avocados, almost all nightshades, corn, and zucchini (I think that is it). I am currently waiting to try coconut and sunflower seeds. On top of this we are vegetarian and you can see my choices are terribly limited. I would consider eating meat, but because of her issues with dairy and eggs I would be very reluctant to try cow and chicken. On top of that I would worry about what the animal had eaten. So, right now remaining veg seems smart. I have to make everything I eat from scratch. It is time consuming and difficult and I am hungry sometimes, but it can be done.