Drain the beans and set aside. In a bowl, whisk together the brown sugar, mustard, water, and bourbon until the sugar is dissolved. Set aside.
Cook the bacon until crisp in a large Dutch oven over medium heat. Remove the bacon and all but a couple of tablespoons of the bacon grease. Add the drained beans to the pot and stir in the bourbon sauce mixture. Bring the beans to a boil, then reduce the heat to low to maintain a gentle simmer. Cover and cook the beans, stirring every 20 minutes, until the beans are soft and the sauce is very thick, about 4 hours. Once the beans are cooked, season them with salt and pepper, to taste. Stir in the cooked bacon and cook, covered, an additional 15 to 20 minutes. Transfer the beans to a serving bowl and serve warm.
If the beans get too dry, add water, 1/4 cup at a time. If the beans are too wet and runny, remove the lid and cook, stirring often, until desired consistency is reached.