Preheat oven to 350 degrees.
In a large pan, add diced bacon. Cook over medium-high heat until fat renders, and bacon begins to crisp. Once cooked, remove bacon and place into a small bowl. Discard bacon drippings, leaving 2 tablespoons in the pan.
Add butter to the pan with bacon drippings, cooking until melted over the heat. Add 1 cup of the shallots and cook until browned, about 3-4 minutes. Remove shallots, leaving the butter mixture in the pan. Place cooked shallots in the bowl with bacon. Stir in ¼ cup of brown sugar, and 1 teaspoon of smoked paprika to create topping.
Add the remaining ½ cup of shallots and green pepper to the pan. Cook until vegetables have softened, about 3-4 minutes.
Stir in tomato sauce, ketchup, molasses, mustard, the remaining 3/4 cup of the brown sugar, garlic powder, Worchester sauce and 3 teaspoons of smoked paprika to create a sauce.
Stir in the beans, and then pour bean mixture into a deep sided 9 x12 baking dish.
Cover dish with foil, and bake in the oven for 30 minutes.
Remove pan from oven and raise oven temperature to 400 degrees. Remove foil, and place back into the oven, about 20-25 minutes or until sauce is thick and bubbly.
Sprinkle on bacon topping, continuing to cook for 10 additional minutes or until bacon is browned and caramelized.
Remove from oven, and let rest for about 10 minutes before serving.
Alternative Cooking Method: If you don’t want to turn on the oven, bring out the slow cooker! Follow the above instructions, but instead of putting the beans into a casserole dish, place them into the slow cooker and cook on high heat setting for 4 hours. Remove the lid for the last 2 hours, and add the bacon topping during the last 15 minutes of cooking. If an extra crispy bacon topping is desired, place crock in the oven set to broil for 4 minutes.