DS tends to be sensitive to the colors as well, but didn't have troubles that struck us as being color-based on our trip. Though with him it's not generally the yellow that does him in, so that might have been it.
Although Uncrustables don't have coloring in them, I can only imagine that a family with a color-sensitive person in it isn't going to enjoy the REST of the ingredients; it's absolutely forbidden in our household. Sad that they can't just do a NORMAL PB&J sandwich, eh?
We didn't do a dining plan, so DS ordered whatever he wanted. Sunshine Seasons worked for him, and there was a tasty grilled cheese sandwich at Brown Derby. The cheese pizzas on the kid meals weren't bad, and didn't seem to have red coloring in them, so that was good. The pizza at Sanaa he found to be delicious!
Definitely use the specialdiets email (should be found as you make ADRs online, or go in and look at your ADRs and you should find it) and make sure they know about the colors. I'm not really sure that they use kraft for their mac and cheese; it did'nt really taste like it, so you might have nothing much to worry about with that...of course cupcakes, etc will be a problem. You might try babycakes at DTD, because they don't use the artificial colors...we didn't really like them (even though we enjoy gluten-free and vegan cupcakes made at a place out here). We're staying at a villa with a kitchen, so we'll have a chance to make treats on our own...or maybe just run up to Whole Foods and see what they have, dessert-wise, for fun since our son can't have so much at the bakeries at Disney.
Best of luck!