Sort and wash the beans, then place them in a small, heavy-bottom pot or Dutch oven. Add enough water to cover the beans by 2 inches. Bring to a boil over high heat, then reduce the heat to a gentle simmer and cook, loosely covered, until the beans are tender, 1 1/2 to 2 hours. Stir the beans occasionally and check the water level, adding additional water as needed to keep the beans moist as they cook.
While the beans are cooking, cook the salt pork in a frying pan until the fat is rendered and the pork is cooked, 6 to 8 minutes, stirring constantly. Remove and reserve the salt pork, leaving the fat in the pan. Add the chopped onion and garlic to the pan and cook over gentle heat until the onion is translucent, stirring occasionally, 4 to 6 minutes.
When the beans are tender, stir in the cooked salt pork, onions, garlic, parsley, tomato sauce, thyme and red pepper flakes. Taste and add 1 1/2 teaspoons salt and one-half teaspoon pepper, or to taste. Bring the mixture back to a simmer and cook a few minutes to marry the flavors. This makes about 1 1/2 quarts beans, which will keep, covered and refrigerated, up to 1 week. The flavors will improve with time.