Roast:20 mins at 450 degrees F, 2 3/4 hours at 275 degrees F, + 20 minutes at 350 degrees F
Sprinkle beef with 1 Tbsp. salt; cover and chill overnight.
Preheat oven to 450 degrees F. Line a 15x10 baking pan with a silicone baking mat. In a large skillet heat 1 Tbsp. of the oil over medium-low heat. Add bacon; cook and stir until browned. Drain on paper towels, reserving 3 Tbsp. drippings. Place squash in prepared baking pan. Add 1 Tbsp. of the butter and 1 Tbsp. bacon drippings; sprinkle with additional salt. Roast 20 to 30 minutes or until tender and brown, stirring once. Cover with waxed paper; set aside. Reduce oven temperature to 275 degrees F.
Add remaining 2 Tbsp. oil to remaining bacon drippings in skillet; heat over medium-high heat. Pat beef dry with paper towels. Working in batches, cook beef in hot fat until well browned. Remove beef, reserving 1 tsp. drippings.
Add remaining 1 Tbsp. butter to reserved drippings. Add onions. Cook over medium heat 3 to 4 minutes or until nearly tender, stirring to scrape up crusty brown bits. Stir in leek and garlic; sprinkle with additional salt. Cook 4 minutes more, stirring occasionally. Transfer mixture to a 3-qt. baking dish; set aside. Add wine to skillet. Bring to boiling; reduce heat. Boil gently, uncovered, until reduced to 2 cups.
Place beef and bacon on top of onion mixture and dot with tomato paste. Add reduced wine and enough stock to nearly cover beef. Using kitchen string, tie cinnamon, peppercorns, and cloves in a piece of cheesecloth. Tie together parsley stems and inner leek piece. Tuck cheesecloth bag, parsley bundle, and bay leaves into beef mixture; sprinkle with thyme.
Cover baking dish with parchment paper and a triple layer of heavy foil; seal tightly. Place on a rimmed baking sheet. Roast 2 hours. Add prunes. Roast, covered, 45 to 60 minutes more or until meat is easily pierced with a knife. Skim off fat. Remove and discard cheesecloth bag and parsley bundle. Increase oven temperature to 350 degrees F. Add squash. Roast, uncovered, 20 minutes, basting once or twice. Sprinkle with parsley leaves before serving.