Cook bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from pan, and crumble. Add onion to drippings in pan; sauté 4 minutes. Add garlic, and sauté 1 minute. Remove from heat; combine onion mixture and bacon.
Arrange 4 cups bread cubes in bottom of a 13 x 9-inch baking dish coated with cooking spray; top with 2/3 cup cheese, half of onion mixture, and 6 tomato slices. Combine milk and remaining ingredients; stir well with a whisk. Pour half of milk mixture over tomatoes. Top with 4 cups bread cubes, 2/3 cup cheese, remaining onion mixture, 6 tomato slices, and half of milk mixture. Cover; chill at least 1 hour or up to 24 hours.
Preheat oven to 325°.
Bake, uncovered, at 325° for 55 minutes. Sprinkle with 2/3 cup cheese; bake an additional 5 minutes or until cheese melts. Let stand 5 minutes before serving.