My daughter has a cows milk protein allergy. We have had to exclude all sources of cow diary from her diet. At first, I was just going to exclude direct sources of diary... but she was still getting sick, so I had to start reading ingredient labels. Once cows diary products were removed from her diet, her illness and symptoms disappeared. (She had chronic sinus infections, coughing/congestion starting around 11 months. Always on antibiotics, until she started having allergic reactions to antibiotics... If what I went through can help you and your son at all, then I am happy to share what I've found.)
Doctors say that cows milk protein allergy is a common childhood allergy. Most kids outgrow it between age 3-6. Unfortunately, my daughter has not out grown it... maybe she will by the time she's 6-?! (Crossing my fingers!) As an infant, she drank (cows) milk based formula after breast feeding, and then started toddler's formula (also milk based) on her doctor's suggestion because she had started losing weight around 12 months. Of course, the reason she was underweight was because her body couldn't metabolize cows milk... I suspect that one of the reasons she has not outgrown the cows milk allergy yet is because she was overly exposed to cow dairy as an infant (as in, the longer a child is exposed to the allergen could mean that it takes longer for him to outgrow it.)
My daughter drinks whole goat milk, goat yogurt, goat butter, sheep/goat cheese. Most grocery stores (here in Texas) have Mendelson's Goat Milk (purple container) and carry a few flavors of goat yogurt (Rosewood Hill Farms is a common brand) or they will order it. I bought a bread machine so I can make bread with goat milk, since grocery store bread contains (cows) milk. (Note: true french bread is made with water, but it might be a bit hard for a young child to chew.) I cook with olive oil instead of butter. My husband and I have a hard time with the taste of goat diary (compared to cow dairy), but since my daughter has been on it since 18 months, she doesn't know the taste difference.
There is research that shows a correlation between children who are allergic to soy are also allergic to cows milk protein. However, that does not mean all children are also allergic to soy. If you notice digestive issues, etc., soon after introducing soy to your son, then you might want to exclude soy protein from his diet also.
Feeding soy to children is a controversial topic; different people have different opinions. Some children can't eat goat diary nor cows diary and soy is the only option... Personally I am not a fan of feeding children large amounts of soy. Soy protein is interpreted by the body as the female hormone estrogen. I have concerns on what the long-term effects of soy protein would be on my daughter (estrogen does a lot more than just direct female reproductive organs; it influences how and where the body stores fat, how muscles develop, and other hormones may get raised due to elevated levels of estrogen in a body... Besides, I feel my daughter gets more than enough soy in her diet from foods made with vegetable oil.) However, I thought I should mention the soy controversy so you can do your own research and decide what is best for your family.
There is nothing fun about a food allergy... You definitely have to cook at home more. However, a cows milk allergy is manageable compared to other food issues. Good luck. Feel free to message me is any of this was helpful and you have questions.