Preheat oven to 350 degrees F.
In a large skillet heat 2 tablespoons olive oil over medium heat, add the sliced onion and minced garlic, saute for about 2 minutes. Then add the chicken slices and cook until chicken is a nice golden brown. Turn the heat up a touch and add the bell pepper slices and dried chili flakes. Once chicken is no longer pink remove from the heat and place the mixture into a bowl.
In a small skillet add 1 cup oil. When oil is warm submerge a tortilla for 10 to 15 seconds or until soft. This will soften them and make rolling a lot easier. Drain on paper towels and repeat this process until all tortillas have been softened. Pour 1 cup of Green Sauce on bottom of the baking dish to cover. Divide the chicken mixture evenly among the tortillas, roll them up. Place seam side down on top of the sauce in the baking dish. Pour the remaining green sauce over them and spread the cheese mix evenly over the top. Bake for about 20 minutes until golden brown. Remove from the oven and serve with long-grain rice.
For the Green Sauce:
Pulse all ingredients in a food processor until a nice salsa consistency is reached.
For the Rice: Pour 3 cups of hot water in a large saucepan and bring to a boil. Rinse the rice well in a bowl under cold water and drain. This will remove surface starch and will be less sticky. Place the rinsed and drained rice into the saucepan, cover and cook until al dente, about 10 to 15 minutes. Add fresh cilantro and lime juice and serve.