Melt butter in a large saucepan over MED heat. Sprinkle in flour and whisk to combine. Mixture will look like very wet sand. Cook for approximately 1 minute, whisking often. Slowly pour in about 2 cups or so of the milk/half and half, while whisking constantly, until smooth. Slowly pour in the remaining milk/half and half, while whisking constantly, until combined and smooth.
5 Continue to heat over MED heat, whisking very often, until thickened to a very thick consistency. It should almost be the consistency of a semi thinned out condensed soup.
6 Remove from the heat and stir in spices and 1 1/2 cups of the cheeses, stirring to melt and combine. Stir in another 1 1/2 cups of cheese, and stir until completely melted and smooth.
7 In a large mixing bowl, combine drained pasta with cheese sauce, stirring to combine fully. (It will look like a lot of sauce, but will thicken a lot during baking.) Pour half of the pasta mixture into the prepared baking dish. Top with 1 1/2 cups of shredded cheeses, then top that with the remaining pasta mixture.
8 Sprinkle the top with the last 1 1/2 cups of cheese and bake for 15 minutes, until cheesy is bubbly and lightly golden brown.