Preheat the oven to 375F degrees. Bring a medium pot of salted water to a boil. Add the noodles and cook until just al dente (about 6 minutes), according to package directions. Drain and set aside.
Meanwhile, heat the butter in a saucepan over medium heat. Add the flour and cook to make a golden brown paste, stirring often. Gently whisk in the milk and cook, stirring until the milk thickens, about 5 minutes. Stir in the fontina, Swiss cheese, and 2 tablespoons of Parmesan, until melted. Add the ¼ teaspoon cayenne pepper, about ½ to 1 teaspoon of salt, and freshly ground pepper to taste.
In a large bowl, toss together the cooked noodles, cheese sauce, peas and asparagus. Stir until the noodles and vegetables are coated. Stir in the basil and ½ cup of the mozzarella balls. Place in a 9x9-inch baking dish. Then sprinkle the remaining ¼ cup mozzarella balls over the top.
Mix together the breadcrumbs, Parmesan cheese, and another ¼ teaspoon cayenne pepper. Bake for 20 minutes or until hot and bubbly. Remove from oven and let set for 5 minutes for the sauce to thicken back up before serving.