Lightly spray a 9×13 inch glass baking dish with nonstick cooking spray. Set aside.
In a large frying pan, heat the olive oil and sauté the red pepper, onion, and sausage. Combine the cooked sausage mixture with 1 1/2 cups of the shredded cheese.
Lay a tortilla flat on a plate. Scoop about ⅓ cup of the sausage mixture on the tortilla. Roll up tightly and place the enchilada seam side down in the baking dish. Repeat with the rest of the tortillas.
In a separate bowl, whisk together the eggs, milk, flour, salt, and cayenne pepper. Pour the egg mixture over the tortillas; sprinkle with remaining cheese. Cover the dish with foil and refrigerate overnight.
In the morning, preheat the oven to 350 degrees. Bake (with foil on), for 40 minutes. Remove the foil; bake for 15 minutes more, until the cheese is melted, the eggs are set. The enchiladas will be golden on top. Garnish with tomatoes, sour cream, cilantro, or salsa.