1. Place beans in a large bowl and cover with cold water. Let soak overnight, 8 hours minimum. If you don't have time to let them stand overnight, boil with a half-gallon of water for 2 minutes and let stand, covered, for 1 hour.
2. Drain and rinse beans. Place in slow cooker.
3. Heat oil in a large nonstick skillet over medium-high heat. Add onions and sausage. Cook until onions are softened and light golden and sausage is browned on the outside, about 5 minutes. Add garlic, thyme and crushed red pepper; cook for 1 minute. Add to the beans.
4. Add molasses, tomato puree, Worcestershire sauce and mustard to the beans; stir to combine. Add boiling water and top with bay leaves.
5. Cover and cook until the beans are tender, about 4 1/2 hours on high or about 11 hours on low. Remove the bay leaves. Season with vinegar, hot sauce, salt and pepper. Serve hot.