Dissolve salt in 2 quarts of cold water in a large bowl. Add the beans and soak at room temperature for at least 8 hours and up to 24 hours — this helps the beans cook evenly and prevents the skins from bursting.

Heat the oven to 350°F with the rack in the lower-middle position. Drain and rinse the soaked beans.

Combine the rinsed beans, water, one halved bell pepper, one halved onion, the halved garlic head, bay leaves, and salt in a large Dutch oven. Bring to a simmer over medium-high heat.

Cover the pot and transfer it to the oven. Bake until the beans are tender but still holding their shape, about 45 minutes to 1 hour.

While the beans cook, finely dice the remaining bell pepper halves and onion halves. Heat the oil in a large skillet over medium-high heat until shimmering, then sauté the diced vegetables until softened and beginning to brown, about 8 to 10 minutes.

Stir the minced garlic, cumin, oregano, and tomato paste into the skillet. Cook until fragrant, about 1 minute, then remove from the heat.

Remove the Dutch oven from the oven and discard the halved pepper, onion, garlic head, and bay leaves. Stir the rinsed rice, the prepared sofrito, and salt into the beans.

Cover the pot and return it to the oven. Bake until the liquid is fully absorbed and the rice is tender, about 30 minutes.

Let the pot stand, covered, for 10 minutes to allow the steam to finish the grains. Stir in the vinegar, sprinkle with scallions, and serve hot with lime wedges.