Melt butter in a medium saucepan and whisk in flour. Cook for 1 minutes over medium heat and slowly pour in milk, whisking continuously. Stir in onion flakes and salt and pepper. Bring to a boil, reduce heat, and simmer for 2 minutes. Meanwhile, in a large bowl toss together shredded cheeses. Remove milk mixture from heat and stir in the American cheese and 1 heaping cup of the mixed cheeses. Mix chopped cooked bacon with remaining shredded cheeses. Combine cooked pasta with the cheese sauce. Pour half into a buttered 3 quart baking dish. Sprinkle with half of the bacon-cheese mixture. Pour on the rest of the pasta and top with the last of the shredded cheese. Bake at 350 for 20-30 minutes or until slightly bubbly and browned on top. Let sit for 10 minutes before serving.
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