1. Boil the chicken with 1/2 cup onion and the salt and pepper until meat falls off the bones (about 1 hour), save the chicken stock for use later. Let the chicken cool, then slice the into 1/4 to 1/2 inch cubes.
2. Mix 1/2 cup of the chicken stock with all the other remaining ingredients except the cheese and tortillas.
3. Mix the three cheeses together.
4. Dip tortillas into remaining reserved chicken stock and put a double layer of tortillas in two 8 inch x 8 inch pans (I use two 2 quart Pyrex glass ones), a layer of the soup, vegetables and chicken mixture, a layer of 1/3 of the cheese, then repeat these layers two more times.
5. Cover with tinfoil and bake at 300 degrees for 1 hour.
6. Let the dish set for 10 minutes before serving. This recipe results in a mildly hot dish. If you would like it hotter, increase the three peppers, or just serve with a jar of ground cayenne pepper, so each person can adjust the heat as they like.