RINSE beans. Soak the beans in a pot either by covering with water 2 inches above beans and leaving overnight (8 hours) or by covering with 2 inches water and bringing to a boil, covering and removing from heat and letting soak 1 hour. Drain the beans.
PREHEAT oven to 350ºF(180ºC).
IN a large saucepan over medium heat, cook onions in oil until just brown, stirring often. Add tomato paste and cook 2 minutes. Add molasses, sugar, jalapeno, mustard, and red pepper, stirring to combine.
STIR in beans and 4 cups water. Increase heat to medium-high and bring to a boil. Remove from heat.
COVER and bake at 350ºF(180ºC). for 3 hours. stir in remaining 1-2 cups of water and bake another 30-45 minutes until beans are tender.
