1. Preheat oven to 325°.
2. Combine 1 1/4 teaspoons salt and next 4 ingredients (through garlic) in a small bowl. Stir in 1 tablespoon oil. Rub salt mixture evenly over side of beef without fat cap; place beef, salt-mixture side down, in an enameled cast-iron Dutch oven. Combine stock and beer; pour over beef. Cover and bake at 325° for 4 hours or until tender, turning after 2 hours. Cool to room temperature; cover and refrigerate overnight.
3. Preheat oven to 350°.
4. Trim fat cap from beef; discard. Thinly slice beef. Skim fat from cooking liquid; discard fat. Remove 1 cup cooking liquid; set aside. Place beef and remaining cooking liquid in a 13 x 9-inch glass or ceramic baking dish; cover with foil. Bake at 350° for 30 minutes or until thoroughly heated.
5. Heat a large skillet over medium-high heat. Add remaining 2 tablespoons oil to pan; swirl to coat. Add onions; sauté 6 minutes. Reduce heat to medium; cook 15 minutes or until tender, stirring occasionally. Stir in vinegar, sugar, and cornstarch; cook 30 seconds. Stir in reserved 1 cup cooking liquid; bring to a boil. Cook 1 minute, stirring frequently; remove from heat. Stir in remaining 1/4 teaspoon salt and thyme. Serve with beef.