In a large stock pot, combine the beans, onion, bell pepper, garlic, oregano, cumin, bay leaves, and 6 cups of water. Bring to a boil over high heat, then reduce the heat to medium. Partially cover the pot and simmer until the beans are tender, 2 to 2 1/2 hours. Add more water to the pot during the first hour of cooking if it evaporates and the beans are not covered by at least 2 inches of water.
When the beans are tender, remove the lid and turn the heat off. Discard the bell pepper and stir in the vinegar, oil, and salt and black pepper. Taste and adjust the seasoning if needed.