Sort and wash beans; place in a large Dutch oven. Cover with water to 2 inches above beans, and bring to a boil; cook 2 minutes. Remove from heat; cover and let stand 1 hour. Drain beans in a colander, and set aside.
Heat oil in pan over medium-high heat. Add onion, bell peppers, jalapeño, and garlic; sauté for 10 minutes or until tender. Add chili powder, cumin, ground red pepper, salt, and black pepper; sauté 1 minute. Stir in masa harina and cocoa. Add beans and broth; stir well. Bring to a boil; reduce heat, and simmer, uncovered, 2 hours or until beans are tender, stirring occasionally.