Heat oven to 375 degrees. Butter a 13 by 9 inch or 3 quart casserole dish. Remove crust from bread, cut into 1/2 inch cubes, and place in bowls. Melt 2 tablespoons butter over medium heat. Pour melted butter over bread and toss to coat. Put bread cubes into a food processor and process until fine crumbs form. Set bread crumbs aside.
In a medium saucepan over medium heat, heat milk, cream and apple cider until hot.
While milk mixture is heating, melt remaining 4 tablespoons butter in a large high-sided skillet over medium heat. When butter is melted and bubbling, add flour. Cook stirring for 1 minute.
Pour hot milk mixture slowly into skillet with flour-butter mixture whisking constantly. Continue cooking and whisking over medium heat until sauce bubbles and becomes thick.
Remove from heat and stir in 1/2 teaspoon salt, pepper, nutmeg, cayenne pepper, mustard, 2 1/2 cups cheddar and 1/2 cup gruyere. Combine and set aside.
Fill a large saucepan with 3 to 4 quarts of water add remaining 2 tablespoons salt and bring to boil. Add pasta and cook slightly less than what the package calls for. Pasta should be slightly underdone. Pour pasta into colander and rinse under cold water draining well.
Stir pasta into cheese sauce and transfer to prepared casserole dish. Sprinkle remaining 1 1/2 cups cheese over pasta and spread bread crumbs on top to cover. Bake for about 30 minutes or until golden brown on top.