Place the beans and salt in a large saucepan, cover with water by 2 to 3 inches, and soak overnight.
Drain and rinse the beans. Return the beans to the large saucepan and cover with 4 inches fresh water. Bring to a boil, then lower the heat and simmer for 1 1/2 hours, until the beans are tender but not bursting open.
Preheat your smoker to 250°F with 2 chunks of wood.
In a pan over medium heat, cook the bacon until it is almost crisp. Remove the bacon from the pan and dab the slices with paper towels. Reserve about 1 tablespoon of bacon grease in the pan, discarding the rest, then roughly chop the cooked bacon.
Add the onion and bell pepper to the reserved bacon grease and cook on medium heat until translucent. Add the garlic, stirring constantly, and cook for another 2 minutes.
Drain the beans, reserving 2 cups of the bean water. Transfer the beans to a deep, half-size aluminum pan. Stirring the bean mixture thoroughly, add the barbecue sauce, brown sugar, mustard, jalapeño, barbecue rub, and molasses.
Place the beans in the smoker and cook for 5 hours, stirring every hour. Replenish the wood chunks as needed. If the beans start to get too thick, add some of the bean water and stir.
After 5 hours, the beans should look dark and sticky and will be tender, with a slightly creamy texture. Remove the beans from the smoker and serve.