To make the cheese sauce- Melt butter in a large saucepan over medium-low heat. Whisk in flour until smooth. Cook while whisking constantly for 1 minute. Gradually whisk in the milk a little at a time. Cook over medium heat while whisking for 5 minutes or until the sauce has thickened. Remove from heat and whisk in cheddar cheese, green chilies, and salt.
Heat and large skillet to medium-high heat. Add pork sausage and cook until sausage crumbles and is no longer pink. Remove the sausage from the pan with a slotted spoon and drain on paper towels. Drain any excess grease from the pan.
In the same skillet melt butter over medium heat. Add green onions and cilantro, sauté for 1 minute. Add eggs, salt, and pepper. Cook without stirring until the eggs begin to set on the bottom of the pan. Draw a spatula across the bottom of the pan to form large curds. Cook until the eggs are thickened but still moist. Remove from heat and fold in 1 ½ cups of the cheese sauce and the cooked sausage.
Spoon about 1/3 cup of the egg mixture down the center of each tortilla. Roll up and place seam side down in a lightly greased 13×9” baking dish. Pour the remaining cheese sauce over the tortillas. Sprinkle with jack cheese.
Place into the oven and bake at 350 degrees for 30 minutes or until the sauce is bubbly. Remove from the oven and serve with tomatoes, cilantro, and green onions.