Preheat oven to 350 degrees F. Butter your 6-quart casserole dish and set aside. Reserve 1/2 cup of the shredded cheese for the layering we're going to do with it! But I like to set it aside now so I don't forget.
To a medium pot, set over medium heat, add the butter. When the butter has melted, add the flour and mix it together and cook the flour butter mixture for about 1 minute. Pour in the milk in two batches, stirring continuously in between additions.
Cook until it thickens up, about 2 to 3 minutes. It’ll start to bubble up and thicken. Give it a good whisk and be sure to get in those corners of the pan to get any floury bits up and mixed in. It should be thick enough to coat the back of a spoon.
Turn off the heat and whisk in the kosher salt, crushed red pepper, Dijon mustard and a few rounds of pepper. Add the grated cheeses and mix them in until they’re melted. Give it a taste and adjust the salt to taste. Cover the pot with a lid and set aside.
Meanwhile, bring a pot of salted water to a boil. Cook the pasta according to the package’s instructions, about 6 to 7 minutes, until al dente.
Drain the pasta and then immediately run it under cold water to get rid of some of the starch. Give it a shake in the colander to shake off some of the excess water and then add it to the pot with the cheesy sauce. Mix until thoroughly combined.
Add half of it to the prepared baking dish and then sprinkle one layer of cheese. Then add the remaining macaroni on top and smooth it into an even layer and then top it with the reserved bread crumbs and remaining cheese.
Transfer it to the oven to bake for about 40 to 45 minutes, until the macaroni and cheese is bubbling and golden brown on top.