Many hens with egg yolk peritonitis/internal laying have E.coli infections, and this can cause bright yellow stools. In poultry who have 9 air sacs throughout the body, any infection just travels all over. They can get air sacculitis that affects breathing, bone infections which she could have causing lameness, and infection in her belly. Many people will use antibiotics such as penicillin or vets will prescribe Baytril to buy some time. In the end, they may need to be put down. It usually can be confirmed with a necropsy after death, just to know for sure. Just to clarify something in your first post about Mareks, not all chickens with Mareks have eye abnormalities.