Combine milk, green onions, egg substitute, mustard, and pepper in a large bowl, stirring with a whisk. Add bread cubes and ham; stir well to combine. Pour into a 2-quart baking pan coated with cooking spray. Sprinkle with shredded cheese. Cover and chill 8 hours or overnight.
Preheat oven to 350°.
Uncover dish, and bake at 350° for 20 minutes. Sprinkle with bacon. Bake an additional 15 minutes or until bread mixture is set and cheese is bubbly.