Hi there,
My parents returned from a trip to Disney 4 weeks ago. My dad has suffered with Crohn's for over 25 years. In preparation we planned every meal in advance knowing exactly what he would pick at each restaurant. I agree with the poster who said no 2 people have the same trigger items although my dad is on a fairly limited diet. (no whole wheat, no raw veggies, no greens etc.)
With this in mind random counter service can be difficult with the whole wheat buns and fries with skins on them but here is where he ate and what he ate:
Chefs de France - ham and cheese quiche with fries subbed for the side instead on salad. He really enjoyed this and didn't find it heavy.
ESPN Club - Burger without the lettuce and tomato with fries
Rose and Crown - Fish and Chips
Le Cellier - New York strip cooked plainly with the steak fries
Sci-Fi - burger without the toppings and fries
Liberty Tree Tavern - the Thanksgiving dinner (he didn't eat the salad, beans or stuffing but was stuffed on the potato, mac and cheese, meat and rolls - the table came with 6, he had 5 of them. They also gave him plain ice cream for dessert since he couldn't have the crisp)
Main Street Bakery - ham sandwich with the lettuce and tomato taken off (this was the same day as LTT so the smaller lunch left lots of room for supper)
Earl of Sandwich - club sandwich with just the meat and regular mayo, no lettuce or tomato
Yak and Yeti Counter Service - chicken balls with sweet and sour sauce and white rice, he just didn't eat the peppers and onions
Grand Floridian Cafe - Breakfast - the All-American but no sausage as that was deemed to be spicy
The Plaza - Club sandwich without the lettuce and tomato on sourdough bread with fries
La Kringla - Roast beef sandwich with swiss cheese. The onion was taken off.
snacks included: Milk shake from Min and Bill's in DHS, pineapple dole Whip, Rice Krispie treat from Goofy's, cloudhorn from Norway
Fries at the above locations did not have skins and the burgers had white buns.
If in doubt, just ask. Disney is awesome at accommodating special needs.
Have a wonderful time!