Preheat the oven to 350 degrees Fahrenheit and lightly coat a 13x9 inch baking dish with cooking spray.
In a large skillet over medium heat melt the butter. Add the onion, red and green bell peppers, and jalapeno; and cook, stirring occasionally, until the vegetables become tender, about 4 minutes. Add the garlic, chili powder, cumin, oregano, cayenne, salt, and black pepper; cook, stirring constantly, for about a minute.
Sprinkle the flour over the vegetable mixture; cook, stirring constantly, for about 1-2 minutes. Stir in the broth and milk and bring to a boil, stirring constantly. Boil, stirring occasionally, until thickened, about 2 minutes. Remove from the heat, and stir in the tomatoes, green chiles, and sour cream. Stir in the chicken and mix to combine.
Combine the cheeses in a bowl. Heat the tortillas in the microwave for about 30 seconds.
Line the bottom of the prepared baking dish with 6 tortillas, overlapping slightly, to cover the bottom of the dish. Top with half of the chicken mixture, one-third of the cheese, and 6 more tortillas. Top with the remaining chicken, one-third of the cheese, and remaining 6 tortillas. Sprinkle with remaining one-third cheese. Cover with lightly greased aluminum foil.
Bake covered for 20 minutes. Uncover and bake until the cheese is lightly browned and melted, 5 to 10 more minutes. Let stand 10 minutes before serving. Sprinkle with the cilantro. Top with the desired toppings.