Step 1: Cook the Macaroni. Bring a large pot of salted water to a rolling boil. Add the elbow macaroni and cook according to package directions until al dente, usually 7-9 minutes. Drain well and set aside. Do not rinse.
Step 2: Prepare the Roux. While the pasta cooks, melt the butter in a large, heavy-bottomed pot or Dutch oven over medium heat. Once melted, add the flour and whisk constantly for 1-2 minutes until a smooth paste (roux) forms and turns a light golden color.
Step 3: Whisk in Milk. Gradually whisk in the warmed whole milk, a little at a time, ensuring no lumps form. Continue whisking constantly until the sauce thickens and begins to simmer, about 5-7 minutes.
Step 4: Season the Sauce. Remove the pot from the heat. Stir in the salt, black pepper, ground mustard (if using), and cayenne pepper (if using). Taste and adjust seasonings as needed.
Step 5: Add the Cheese. Add the shredded cheddar and Gruyère (or your chosen cheeses) to the sauce in batches, stirring until each batch is fully melted and incorporated before adding more. Continue until all the cheese is melted and the sauce is smooth and creamy.
Step 6: Combine Pasta and Cheese Sauce. Add the cooked, drained macaroni to the cheese sauce. Stir gently until all the pasta is evenly coated with the rich, creamy cheese sauce.
Step 7: Bake (Optional, but Recommended for a Golden Crust). Pour the mac and cheese into a greased 9x13 inch baking dish. Bake in a preheated oven at 375°F (190°C) for 20-25 minutes, or until bubbly and golden brown on top. For extra crunch, sprinkle with buttered breadcrumbs before baking.