Step 1

In a large bowl, stir the beans with 2 quarts water and 1 tablespoon salt. Cover and soak for 12 to 24 hours. When ready to cook the beans, heat the oven to 275°F with a rack in the lower-middle position. Drain the beans and transfer to a Dutch oven. Stir in 5 cups water, the guajillo chilies, half of the onion, half of the garlic, the oregano and 1½ teaspoons salt.

Step 2

Bring to a boil over medium-high; as the mixture heats, use a wide, flat spoon to skim off and discard any scum on the surface. Once boiling, stir, then cover and place in the oven. Cook until the beans are creamy and tender but still retain their shape, 1½ to 2 hours. Remove the pot from the oven, uncover and stir. Return to the oven, uncovered, and cook until the liquid has reduced slightly and the color of the beans has deepened by a few shades, about another 1½ hours.

Step 3

Meanwhile, in a 12-inch skillet over medium, heat the oil until shimmering. Add the remaining onion, remaining garlic, ½ teaspoon salt and ¼ teaspoon pepper; cook, stirring, until lightly browned, 6 to 8 minutes. Add the tomatoes and cook, stirring, until the sofrito is soft and jammy, 11 to 12 minutes. Set aside off the heat.

Step 4

When the beans are done, remove the pot from the oven. Using tongs, transfer the chilies to a cutting board; mince and return them to the pot. Stir in the sofrito, then taste and season with salt and pepper.