Sounds like your doc is on top of things--blood tests are just a way of narrowing the suspects. A lot of allergies/intolerances will not show up on tests and the only way to be sure is to do an elimination/addition test. Eliminate suspect foods until you reach baseline and then test them individually for a reaction. If you get a reaction then eliminate the food again and test again at a later date just to be sure it wasn't coincidence.
Personally, with my daughter we eliminated all suspect foods at once and added them back in starting with the least likely item on the list (soy, dairy, gluten, strawberries, tomatoes, legumes)--Turns out she definitely reacts to soy, and probably dairy (results are a bit mixed here) :/
If eliminating all your suspect foods at once seems daunting, you can continue to eliminate one item at a time until you reach baseline, but it may take longer. (Note: Once you eliminate a food item do not reintroduce it until you get to baseline, because your son could be reacting to more than one thing.)
Also, make sure to double check your son isn't getting exposed any hidden dairy (or whatever else you eliminate) in packaged foods (beware of lunch meats, hotdogs, dressings, etc), OR through soaps, lotions, shampoos etc.
One more thing--if you happen to be breastfeeding him, make sure you aren't consuming anything you have eliminated from your son's diet.