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.
Preheat oven to 350°.
Cook bacon in a Dutch oven over medium heat 5 minutes or just until crisp. Remove bacon from pan, reserving 1 tablespoon drippings in pan; return bacon to pan. Add onion to drippings in pan; cook 5 minutes or until onion begins to brown, stirring often. Add tomato paste; cook 2 minutes, stirring often. Add molasses, sugar, jalapeño, mustard, and red pepper; stir to combine. Stir in beans and 4 cups water. Increase heat to medium-high; bring mixture to a boil. Remove from heat. Cover and bake at 350° for 3 hours. Stir in remaining 1 cup water. Cover and bake an additional 1 hour or until beans are tender, but not falling apart, and liquid is almost absorbed. Remove from oven; stir in salt.