Heat oven to 375ºF (190ºC). Butter a 3-quart casserole dish; set aside. Place bread crumbs (2 cups), Parmesan cheese (1/4 cup), and dried thyme leaves (1/2 teaspoon) in a medium bowl. Melt 2 tablespoons butter. Pour the butter into the bowl with the bread mixture, and toss; set breadcrumbs aside.
In a medium saucepan set over medium-low heat, heat milk (5 1/2 cups).
Melt the remaining 6 tablespoons of butter in a high-sided skillet over medium heat. When butter bubbles, add flour (1/2 cup). Cook, whisking constantly, for 1 minute.
While whisking, slowly pour in hot milk. Continue cooking, whisking constantly, until the mixture bubbles and becomes thick.
Remove pan from heat. Stir in salt (2 teaspoons), nutmeg (1/4 teaspoon), black pepper (1/4 teaspoon), cayenne pepper (1/4 teaspoon), 1 ½ cups sharp cheddar cheese, 1 ½ cups sharp white cheddar cheese, and 1 ½ cups Gruyere; set cheese sauce aside.
Fill a large saucepan with water; bring to a boil. Add macaroni (1 pound); cook 2 to 3 minutes less than the manufacturer's directions, until the outside of the pasta is cooked and the inside is underdone. (Different brands of macaroni cook at different rates; be sure to read the instructions.) Transfer macaroni to a colander, rinse under cold running water, and drain well. Stir macaroni into the reserved cheese sauce.
Pour mixture into prepared dish. Sprinkle remaining 1 cup sharp cheddar cheese, 1/2 cup sharp white cheddar cheese, 1/2 cup Gruyere, and breadcrumbs over top. Bake until browned on top, about 30 minutes. Transfer dish to a wire rack to cool for 5 minutes; serve hot.