Review all recipe notes and instructions before beginning.
Preheat the oven to 400 degrees.
Melt 1 Tablespoon of butter in a large skillet over medium high heat. Add the ground beef, salt, and pepper and sauté for 2-3 minutes. Add the mushrooms. Sauté for a couple of minutes. Lastly, add the peppers, onions, garlic, worcestershire, and ketchup. Cook until most of the water has evaporated from the vegetables.
While the meat finishes cooking, cook the pasta one minute less than the instructions on the package in salted water. (For reference, mine says to cook for 9 minutes, so I boil it for 8 minutes).
In a medium saucepan, melt 3 Tablespoons of butter over medium heat. Whisk in the flour until a smooth paste forms. Add the milk and whisk until the mixture begins to thicken. It should come to a simmer.
Turn the heat to low. Stir in the salt, american, and shredded cheddar cheese. Continue stirring until the cheese is melted. Stir in the jalapeños.
Grease a 9 x 13 inch baking dish. Pour about 1 cup of the cheese sauce into the bottom. Stuff each shell with beef filling. Place into the dish.
Pour the remaining sauce on top.
Sprinkle the cheddar cheese cubes on top.
Bake for 15-20 minutes or until the edges begin to bubble.