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Preheat oven to 325 F and grease a 9x13 baking pan. Set aside.
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Bring a large pot of water to a boil. Add the pasta and cook 1 minute less than the package directions. Drain pasta.
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Mix the cheeses together. Separate into 3 bowls. 3 cups for the sauce, 1 ½ cups for the inner layer and 1 ½ cups for the topping.
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Melt the butter in a large saucepan over medium heat. Sprinkle in the flour and whisk to combine. Mixture will look like very wet sand. Cook for 1 minute, whisking often. Slowly pour in 2 cups of the half and half, while whisking constantly, until smooth. Slowly pour in the remaining half and half and milk, while whisking constantly, until combined and smooth.
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Continue to heat over medium heat, whisking often, until thickened to a very thick consistency.
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Remove from heat and stir in the spices and 1 ½ cups of cheese, stirring to melt and combine. Stir in another 1 ½ cups cheese and stir until completely melted and smooth.
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In a large mixing bowl, combine pasta with the cheese sauce, stirring to combine fully. Pour half of the pasta mixture into the prepared baking dish. Top with 1 ½ cups of shredded cheeses, then top with remaining pasta mixture.
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Sprinkle the top with the last 1 ½ cups of cheese and bake for 15 minutes, until cheese is bubbly and lightly golden brown.