Place beans in a large bowl, and add water to cover by 2 inches. Cover bowl, and let soak at least 8 hours or up to 12 hours. Drain well.

Stir together beans, 5 cups water, 1 onion half, 1 bell pepper half, and 2 bay leaves in a large pot or a programmable pressure multicooker (such as Instant Pot); bring to a boil over medium-high. Reduce heat to low; cover and simmer until beans are almost tender, 45 minutes to 1 hour. Remove and discard onion, bell pepper, and bay leaves.

Meanwhile, finely chop remaining onion and bell pepper halves. Smash garlic cloves on a cutting board using the flat side of a chef’s knife. Sprinkle garlic with 1 teaspoon salt; rub salt into garlic using side of knife to form a paste.

Heat ¼ cup oil in a large skillet over medium. Add chopped onion, chopped bell pepper, and garlic paste; cook, stirring occasionally, until onions are softened, about 8 minutes. Stir in wine, cumin, oregano, tomato paste, and remaining 2 bay leaves. Cook, stirring constantly, until tomato paste is incorporated and wine is evaporated, 2 to 3 minutes.

Uncover beans, and stir in onion mixture, black pepper, and remaining 2 teaspoons salt. Increase heat to medium; simmer, stirring occasionally, until beans are tender and liquid is thickened, about 30 minutes.

Season beans with additional salt to taste, and drizzle with remaining 2 tablespoons oil. Garnish with cilantro, if desired, and serve with lime wedges.