In a large bowl, combine the red wine, beef stock, brandy, onion, carrots, garlic, parsley sprigs, thyme, rosemary, peppercorns, cloves, allspice, and bay leaf and stir well. Add the beef and stir. Refrigerate, covered, overnight.
Drain the beef and reserve the marinade and vegetables separately. Pat the beef dry with paper towels. Set the beef and vegetables aside.
Preheat the oven to 275 degrees F.
Remove the outer rind of the slab bacon. Cut the bacon into lardons: 1 inch long strips about 1/4- inch thick. In a small saucepan, cover the lardons and the rind with cold water and bring to a boil. Lower the heat, and simmer for 3 minutes. Drain the lardons and rind, pat them dry, and reserve both.
Heat 2 tablespoons of butter and olive oil in a large Dutch oven over medium heat. Add the lardons and cook, stirring, until crisp and their fat has rendered. Using a slotted spoon, transfer the lardons to paper towels to drain.
Season the beef with salt and pepper, dredge in the flour, and shake off any excess.
Raise the heat to high and, working in batches, brown the beef. Using a slotted spoon, transfer the beef to a plate. Pour off all but 1 tablespoon of fat and return to high heat. Add the reserved vegetable mixture and tomato paste and cook, stirring occasionally, until well browned, about 5 minutes.
Return all of the browned beef to the pot. Add the reserved marinade liquid, and reserved bacon rind. Bring to a boil and season with salt and pepper. Transfer the stew to the oven and cook, covered, until the beef is very tender, about 3 hours.
Remove the stew from the oven. Using a slotted spoon, transfer the beef to a plate. Strain the liquid and discard the solids. Return the beef and strained broth to the Dutch oven with the lardons.
Put the pearl onions in a skillet with 1 tablespoon of butter and the sugar. Cover the onions with water and season with salt and pepper. Simmer the onions over medium-high heat until almost tender. Raise heat to high, and reduce the cooking liquid to about 2 tablespoons. Continue to cook the onions, shaking the pan over the heat, until the onions are golden brown and glazed. Transfer the onions to the stew.
Heat 3 tablespoons of butter in another skillet over medium-high heat. Add the mushrooms and season with salt and pepper. Cook the mushrooms, tossing often, until golden brown, about 7 minutes. Transfer the mushrooms to the stew.
In a small bowl, cream together the tablespoon of softened butter with the tablespoon of flour. Roll the mixture into pea-sized pieces.
Bring the stew to a simmer and, while stirring gently, add enough beurre manie, bit by bit, to lightly thicken the sauce.
Divide the stew among 6 shallow soup plates and garnish each with a crouton. Serve immediately with pasta or boiled potatoes.
Preheat the oven to 400 degrees F. Brush both sides of the bread with the butter and arrange them on a baking sheet. Bake the croutons until golden brown. Dip the edges of the bread in the stew to moisten; then in parsley to lightly coat the edges.