Pretty much every resort CS other than CSR (I don't know if they do them or not) and AoA (they do Nemo waffles) can make Mickey waffles. Most Disney owned TS restaurants that serve breakfast can also do Mickey waffles with the exception of CRT, Crystal Palace and Akershus I think.
Pretty much every resort CS other than CSR and AoA has the allergy chicken tenders. In MK you can get them at Columbia Harbour House. In Epcot you can get them at Electric Umbrella and in the American Pavillion in the World Showcase. In AK I'm really not sure if you can get them anywhere or not; we always eat either TS at Tusker House or CS at Flame Tree BBQ and they don't have them at either of those. In DHS I think they have them at most CS locations that are full CS rather than just a window with the exception of Starring Rolls. Most Disney owned TS restaurants also have the allergy tenders, though now that I think about it, I'm not so sure they do in MK. LTT and the Plaza didn't have them when I asked. When we ate at Tony's we wanted the spaghetti with meatballs so I didn't ask and it's been ages since we ate at CRT or CP.
I really don't know where they have the mac & cheese since my kids and I can't eat it due to other allergies.
We LOVE the Polynesian and 'Ohana for breakfast is great. At 'Ohana she'll get fruit, Mickey waffles, eggs, bacon, sausage and breakfast potatoes. When we stay at Poly we really don't eat often in Captain Cook's but when we do they've taken great care of us. We always get the chicken tenders with fries at least once but we've in the past been able to get grilled cheese, hamburgers and an asian noodle bowl. If it's something she likes, Kona Island Sushi Bar makes some really nice sushi and they do have San-J GF tamari which is what they used in the asian noodle bowl (the chef said he actually cooked it in Kona's kitchen but brought it down to us at Captain Cook's). Kona's also always been good. I really enjoyed my Tonga "sliders" which was the version of Tonga Toast that the chef came up with for me.