K.Z.
Sounds like fruits and veggies would be the way to go. How about meat, chicken, eggs etc? Beans also provide some protein. Combining beans with a grain (in your case, one that doesn't contain gluten) makes a more complete protein.
For grains, try rice, quinoa, corn meal (polenta, mush); I have heard of teff but never tried it.
As for the milk substitute, I am reading a book called The Whole Soy Story, and it makes me not want to eat/drink soy. Have you tried almond milk? We don't have known allergies but we tried some just for fun, and it isn't too bad.
FWIW, I have read that we are often most allergic to the foods we crave, so you may be on the right track by eliminating dairy, if you say he loves it.
While you are somewhat limited (and you WILL become a label-reader, whether you want to or not), there should be enough things for him to eat that he won't waste away.
Try googling "nourished kitchen" for recipe ideas, I think they have a section on allergen-free recipes.
Good luck, and let us know what happens!
K. Z.