Hi Linda! Disney is quite aware that many of their guests have food allergies or intolerances and they do all they can to still make it a wonderful culinary vacation for them.
Please refer to the Disney page on their website discussing food issues and suggestions for dining especially for Quick Service locations. Please click
HERE. All of the Disney owned locations will work extensively with you and the chefs will make some amazing alternatives when needed. It is highly suggested that you contact them at least 14 days out by email,
SpecialDiets@DisneyWorld.com or call them directly at 407-824-5967. They will be more then happy to work with you on any of your advanced dining reservation locations which is ultimately the best way to get what you want. Note the allergies on your reservation but also call or email ahead. Once you arrive make sure you talk with a chef before ordering.
Some of the Epcot and a few of the Downtown Disney restaurants are not officially run by Disney so your service and food can be hampered. I have read reviews that Via Napoli in Italy in Epcot does not serve good gluten free choices.
Being aware of your son's needs during your park days will be most important to having a happy child on vacation. Stop in at Guest Services in each park when you arrive and talk with them about what they can do to help with your day. They will likely issue you a Guest Assistance Card which is not necessarily a front of the line pass but it will offer some alternative waiting in line away from the busy crowds. Take the time to go over the attractions you are considering as they can give you insight on the noise levels and the darkness affects they might have.
Enjoy the moment in each park and let your son guide you to when it is time to head back to the resort!