Boil the pasta for about 10 minutes, or until al dente, drain. Return to the pan you boiled it in and set aside.
While the pasta is boiling, make the sauce: In a medium saucepan over medium heat, melt the butter. Add the flour, salt, and black pepper. Whisk constantly over medium heat for about three minutes. Continue stirring with the whisk and slowly pour in the milk. Over medium high heat, whisk the mixture until it begins bubbling and thickening; continue for about 30 seconds whisking. Add mustard, 2 cups cheddar, 2 cups fontina, jalapenos, and hot sauce, whisking until the cheese has melted and completely combined.
Pour sauce over the pasta and toss gently until coated well.
Lightly grease a large baking dish. Add half the noodles and sprinkle half of the remaining cheeses on top. Add the remaining pastas and sprinkle remaining cheese on top of the pasta.
Bake at 375 degrees for about 25-30 minutes or until bubbly and golden brown.