Preheat oven to 325 degrees. Combine chilies and cheese in a well greased 1 qt. casserole dish. Beat egg yolks and set aside. Beat egg whites until stiff and then fold in yolks. Gently mix in the milk, flour, salt and pepper. Pour egg mixture over cheese and chilies. Bake for 30 minutes. Remove from oven and arrange tomatoes on top. Bake for an additional 30 minutes or until knife comes out clean. Let cool for 10 minutes before serving.