1.In a large container, whisk together 2 quarts water and salt until salt has dissolved. Add beans, cover, and let stand overnight at room temperature. Drain and rinse beans.
2.Place a large dutch oven over medium-high heat. Add bacon and cook until fat has rendered and bacon has crisped, 7-10 minutes. Transfer bacon to a paper towel-lined plate, leaving as much fat in dutch oven as possible.
3.Add onion to dutch oven and cook, stirring occasionally, until onion softens and begins to brown around the edges, about 7 minutes. Stir in green pepper, jalapeño, and garlic and cook until fragrant, about 1 minute. Stir in 3 cups of water, chicken stock, reserved bacon, and beans. Bring to a boil, then reduce heat to low and simmer for 1 hour. Preheat oven to 300°F while beans are simmering.
4.Stir in ketchup, brown sugar, honey, molasses, mustard, vinegar, barbecue rub, and hot sauce. Cover and transfer to oven. Cook beans for 4 hours, stirring occasionally. Remove cover and cook until beans are tender throughout and sauce has thickened, about 1 hour longer. Remove from oven and let cool for 15 minutes. Season with salt. Serve immediately; alternatively, store in an airtight container in the refrigerator for up to 1 week, or freeze. Reheat before serving.
2 tablespoons kosher salt
1 pound small dried beans, such as great northern, navy, or pinto beans, picked over and rinsed
8 ounces sliced bacon, cut into 1/2-inch strips
1 1/2 cups finely minced yellow onion (about 1 large onion)
2 tablespoons finely diced seeded jalapeño (about 1 medium pepper)
1/4 cup finely diced green bell pepper
1 tablespoon minced garlic (about 3 medium cloves)
2 cups chicken stock or low-sodium broth
1 1/2 cups ketchup
2/3 cup dark brown sugar
1/3 cup honey
1/4 cup molasses
2 tablespoons yellow mustard
1 tablespoon apple cider vinegar
1 tablespoon barbecue rub
1 tablespoon hot sauce