Pick over the beans to remove any rocks. Transfer to a large bowl and cover with at least 2-inches of water. Let soak overnight.
The next day, heat oven to 350°F. Heat a large, oven-safe, Dutch oven with a tight fitting lid over medium-low heat and add the 8 ounces of diced bacon to the dry pan. Let cook, stirring occasionally, until browned and crisp, this could take anywhere from 5-20 minutes.
Add the 1 diced onion to the cooked bacon and increase heat to medium. Cook until the onion is starting to brown. Add 2 diced peppers and cook 5 more minutes, or until peppers become tender.
Drain the soaked beans and rinse well. Add them to the pot along withe the 4 cups chicken broth, 2 pounds diced tomatoes, 2 peeled and chopped apples, 1 cup ketchup, 3/4 cup dark brown sugar, 1/4 cup honey, 1/4 cup molasses, 2 tablespoons Worcestershire sauce, 1 tablespoon kosher salt, and 2 teaspoons ground mustard. Gently stir to combine. Cover and bake in the oven for 2 hours.
Remove pot from the oven, uncover and bake for another 1 1/2-2 hours or until the sauce is thick and the beans are tender, but not mushy. Taste and season with more salt as needed.
Serve hot or let cool, cover and refrigerate to serve later. Beans will keep covered in the refrigerator for up to 5 days. Reheat on the stove with a little more broth or even apple juice, if you have it, if they get too thick. Enjoy!