In a large saucepan or Dutch oven, bring beans, salt and 2 quarts of water to a boil; boil for 2 minutes. Remove from heat; let stand for 1 hour. Drain beans and discard liquid. Return beans to pan. Cover with remaining water; bring to a boil. Reduce heat; cover and simmer for 1-1/2 to 2 hours or until beans are tender. Drain, reserving liquid. In a greased 2-1/2 quarts baking dish, combine beans, 1 cup liquid, onion, molasses, bacon, brown sugar, mustard and pepper. Cover and bake at 325 °F for 3 to 3-1/2 hours or until beans have reached desired thickness, stirring occasionally. Add more of the reserved cooking liquid if needed.