Place chicken in a large skillet. In a small bowl, stir together diced tomatoes, water and chipotle peppers. Cover and cook over medium heat until chicken is fully cooked, about 35 minutes. (You could also let this simmer all day over low heat or in a crock pot.) Shred chicken. Remove chicken with a slotted spoon and set aside.
Meanwhile, cook pasta according to package directions. Drain. In same pot, melt butter. Stir in flour and cook for 2 minutes. Whisk in milk and cook until slightly thickened, about 3 minutes, stirring frequently. Stir in cheese until melted. Add the chicken to the cheese then add the noodles. Stir to coat evenly.