Preheat oven to 350. Spray a 3 quart baking dish that can also withstand the broiler, with cooking spray. Bring a pot of water to a boil for the pasta. Cook according to directions and drain.
Cook bacon until crisp and transfer to a dish with paper towels to drain. Pour out the bacon drippings, reserving 2 tablespoons in the pan, and add 1 tablespoon of butter.
Whisk flour into the butter/bacon fat until smooth and cook until the flour taste is removed, about one minute. Stir in onion flakes, garlic powder, salt, and pepper. Bring to a boil and reduce heat, simmering about 2 minutes. Toss together the shredded cheeses. Remove sauce from heat and whisk in the American cheese slices and about 1 1/2 cups of the shredded cheese mixture. Toss the bacon with the remaining shredded cheese.
Combine the cooked pasta with the cheese sauce. Pour half of it into the baking dish. Sprinkle with a heavy handful of the bacon-cheese mixture. Repeat with one more layer. Melt 3 tablespoons of butter and combine with the bread crumbs. Sprinkle over top. Bake for 20 minutes and then broil for 3-5 minutes to get the top nice a bubbly brown.