Place the soaked beans and soaking liquid in a large Dutch oven or other oven-safe pot. Add the brown sugar, molasses, dry mustard, salt, tomatoes, pineapple, and half the sliced green onions. Stir to combine. Arrange the bacon in a layer on top of the beans. Cover, and bake about 5 hours, until the beans are tender, but not falling apart. Remove the lid during the last 30 minutes to crisp the bacon.