1. Preheat oven to 250°.
2. Combine first 3 ingredients on a lightly sprayed jelly-roll pan. Bake at 250° for 3 hours. Preheat broiler.
3. Bring 6 quarts water to a boil. Add 2 teaspoons salt and pasta; cook 8 minutes or until al dente. Drain.
4. Cook bacon in a saucepan; remove. Cook onion in drippings 4 minutes. Add flour and garlic; cook 1 minute. Stir in 1 cup milk. Gradually add 3 cups milk; bring to a boil. Cook 1 minute, stirring constantly. Remove from heat; let stand 4 minutes. Stir in cheeses. Add 1/4 teaspoon salt, bacon, tomatoes, and chives. Add pasta. Divide among 8 (10-ounce) lightly sprayed ramekins. Combine panko and butter; sprinkle over pasta. Broil 5 minutes.