In a large skillet, cook sausage over medium-high heat, stirring frequently, until browned and crumbly. Remove from pan and pour onto a paper towel -lined plate.
In a large nonstick skillet, melt butter over medium heat. Add eggs, green chiles, salt, pepper, and cumin. Cook, without stirring, until eggs begin to set on bottom. Draw a spatula across bottom of pan occasionally and continue cooking until eggs are thickened but still moist (do not stir constantly.) Remove from heat, and gently fold in the sausage and 1½ cups of the cheese sauce.
Spoon about ½ cup of the egg mixture on each tortilla and roll up. Place seam side down in prepared pan. Pour enough cheese sauce evenly over tortillas, until covered (you might have some cheese sauce left). Sprinkle with pepper jack cheese.
In a heavy saucepan, melt butter over medium-low heat. Whisk in flour until smooth and cook for 1 minute, whisking constantly. Gradually whisk in milk and increase heat to medium. Cook, whisking constantly, until thickened, about 5 minutes. Remove from heat, and whisk in cheese, green chiles, salt, pepper and red pepper flakes.