I have an 18 mo who has intolerances to gluten, cow dairy and legumes (soy, beans, etc). He has always been slight, but I have been more concerned as he is going through a HUGE growth spurt.
Fortunately, I live in Olympia, WA where I can get substitutes for just about anything.
Pamela's flour and Bob's Red Mill have just about anything I need to make cornbread, muffins and all.
Solid coconut oil is FABULOUS when used as a "butter" on muffins and in banana bread. Olive oil "butter" is great, too ... excellent on potatoes. Both are good as butter substitutes when baking.
Hemp milk has been FABULOUS for protein and more fat than rice milk. I have to be careful with coconut milk as so many brands have a TON of sugar in them. Coconut yogurt has definitely to much sugar.
He is eating lots of salmon (smoked is favorite) and anchovies.
We add 5g of rice protein powder and 1/2 tsp fish oil (berry flavored) in a daily smoothie.
He HATES Hass avocados, which are the most common. The mellower flavored ones are nicer for him, but hard to find. I have discovered, however, that grape juice will disguise about any flavor so grape juice/avocado smoothies it is! Mmm mm.
We go to a naturopathic ped for general check ups and health advice. She has the lo on probiotics to help his guts build up the helpful flora he'll need. When he's about 2 1/2 - 3, we'll start working on increasing his tolerance.
BTW, my mom was giving me grief about delaying building up his tolerance and this article came out in our paper today. Send it to any pushy grandparents you may have:
http://www.theolympian.com/nationworld/story/788154.html