Preheat oven to 350°.
Place tomatoes, onion, and garlic in a food processor or blender; process until onion is minced.
Place tomato-onion mixture, diced tomatoes and green chiles, cumin, and crushed red pepper in a large nonstick skillet; bring to a boil. Reduce heat; simmer, uncovered, 15 minutes. Reserve 1 cup tomato sauce to serve with baked casserole. Set remaining tomato sauce aside.
Combine milk and sour cream in a bowl; stir with a whisk until blended.
Arrange 18 tortilla halves in a 13- x 9-inch baking dish coated with cooking spray; top with half of chicken, half of tomato sauce, and half of sour cream mixture. Arrange remaining tortilla halves over sour cream mixture; top with remaining chicken, half of tomato sauce, and sour cream mixture. Sprinkle with cheese. Bake at 350° for 30 minutes or until cheese melts. Top each serving with about 1 tablespoon reserved tomato sauce.