Cook sausage until browned and crumbly. Drain well on paper towels. In saucepan over medium heat, whisk flour into 1/3 cup melted butter. Cook one minute. Gradually whisk in milk. Cook 5 minutes whisking until thickened. Remove from heat and stir in cheddar, chilies and salt.
Sauté onion and cilantro in 2 Tbsp. butter. Add eggs, salt and pepper. Cook without stirring until eggs begin to set on the bottom. Draw a spatula across the bottom of the pan to form large curds. Cook until thickened but still moist. Remove from heat; fold in sausage and 1 1/2 cups cheese sauce.
Spoon 1/3 cup egg mixture into center of each tortilla. Roll and place seam side down in baking dish. Pour remaining cheese sauce evenly over tortillas. Sprinkle with Monterey Jack cheese. Bake at 350° for 30 minutes until sauce is bubbly. Garnish with chopped fresh cilantro, quartered grape tomatoes and sliced green onions.