1. Sort and wash beans; place in a large Dutch oven. Cover with water to 2 inches above beans; cover and let stand 8 hours or overnight. Drain beans. Wipe pan dry with a paper towel.
2. Preheat oven to 350°.
3. Heat pan over medium-high heat. Add bacon to pan, and cook for 4 minutes or until crisp. Remove from pan, reserving 1 1/2 tablespoons drippings in pan; crumble bacon. Add onion to drippings in pan; cook for 5 minutes or until onion begins to brown, stirring frequently. Add beans, bacon, 4 cups water, 1/4 cup maple syrup, 1/4 cup bourbon, and next 3 ingredients (through pepper) to pan. Bring to a boil; cover and bake at 350° for 2 hours.
4. Stir in remaining 1 cup water, remaining 1/4 cup maple syrup, and remaining 2 tablespoons bourbon. Cover and bake 1 hour or until beans are tender and liquid is almost absorbed. Stir in vinegar and salt.