Joi's Cooking Short Ribs Braised in Red Wine with Bacon, Parsnips, and Pearl Onions

6 pounds bone-in short ribs, trimmed of excess fat and silver skin (see illustration below), or bone-in flanken-style short ribs
3 cups dry red wine (full-bodied)
3 large onions, chopped medium
2 medium carrots, chopped medium
1 large rib celery, chopped medium
9 medium cloves garlic, chopped (about 3 tablespoons)
¼ cup unbleached all-purpose flour
4 cups chicken stock or canned low-sodium chicken broth
1 can (15-ounce) can diced tomatoes, drained
1 ½ tablespoons minced fresh rosemary
1 tablespoon minced fresh thyme leaves
3 bay leaves
1 teaspoon tomato paste
Bacon, Pearl Onion, and Parsnip Garnish
6 ounces bacon (about 6 slices), cut into 1/4-inch pieces
8 ounces frozen pearl onions (do not thaw)
4 medium parsnips (about 10 ounces), peeled and cut diagonally into 3/4-inch pieces
¼ teaspoon granulated sugar
¼ teaspoon table salt
6 tablespoons chopped fresh parsley leaves