My daughter (she's 6) loves Kefir, but I'm not sure if it would provide what you are looking for as far as weight gain. Have you thought of calling Whole Foods, or GNC or someplace like that and asking if they have an organic version of PediaSure? That might be worth the effort to prevent allergy probs. My daughter has an allergy to food dyes and Whole Foods almost always has an alternative to any food we are looking for.
Hope this helps!
'M.
-- PS - this might seem crazy, but ask about SlimFast drinks too- if they have more calories than he is getting now, that would also help do the trick. They don't have anything in them to help lose weight, they are just food substitute drinks. Also ask about EnSure. (I would ask the nutritionists first if either of these would work, then when you call the organic groceries you can ask about all 3 if she says they are alright- at least you might have a chance of finding ONE of them in organic or more "natural" form.