Preheat oven to 375 degrees. Butter 84 one-ounce ramekins. In a small pan over medium heat, melt 2 tablespoons butter; toss with bread in a medium bowl.
Heat milk over medium heat until just steaming. Melt remaining butter in a deep skillet over medium heat. When butter bubbles, stir in flour; cook, stirring, 1 minute. Whisking constantly, slowly pour in hot milk, bring to a boil, and cook until thick enough to coat back of spoon.
Remove from heat. Stir in nutmeg, cayenne, 3 cups cheddar, 1 1/2 cups Gruyere, salt, and pepper. Stir in macaroni.
Pour into ramekins. Sprinkle with remaining cheeses and breadcrumbs. Bake until browned, about 30 minutes.
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