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Rinse, sort, and soak the beans. Spread the beans out into a rimmed baking sheet or plate and pick out any debris or broken beans. Transfer the sorted beans to a colander and rinse under cool water. Transfer to a large bowl or 6-quart or larger slow cooker (this eliminates one extra bowl to wash) and cover with 6 cups of cool water. Cover and soak at room temperature 10 to 12 hours.
Drain the beans. Drain the soaked beans and dry the slow cooker insert if needed.
Layer the bacon, beans, and onions. Spread the diced bacon in a single layer in a 6-quart or larger slow cooker. Add the drained beans, and sprinkle the onions over the beans (do not stir). Cover and turn on to the LOW setting while you prepare the sauce.
Make the flavorful sauce. Place 3 cups of water, the tomato paste, molasses, brown sugar, vinegar, and mustard in a large bowl and whisk until smooth. Reserve the salt for seasoning later in the cooking process.
Pour the sauce over the beans. Pour the sauce evenly over the onions, beans, and bacon. Do not stir.
Cover and cook on low for 6 to 8 hours. Cover and cook on the LOW setting for 6 to 8 hours. At the 6-hour mark, begin tasting for doneness and add the salt as needed. The beans are ready when they are creamy and tender.
Stir and serve. Stir to combine — the sauce will be thick. Serve or cool and refrigerate.