Place the rooster/chicken in large bowl, pour chicken stock and red wine, cover with plastic wrap and marinade for at least 2 hours or overnight.
Add the bacon to a large pot over medium-high heat. Cook until the bacon is crispy, about 8 minutes, then remove it from the pan with a slotted spoon.
Remove chicken from the wine marinade, (save the marinade). Pat chicken pieces with paper towels until very dry. In the same pot that you cook the bacon, add half of the olive oil and heat over medium heat until it’s just about to smoke. Working in batches if necessary, add chicken in a single layer and cook until well browned, 3 to 5 minutes per side. Transfer chicken to a plate as it browns.
Add rest of olive oil to the pot, add chopped onions, garlic and carrots and let them cook until the onions are golden brown, about 5-6 minutes.
Push the vegetables to the side of the pan and add the tomato paste. Cook the tomato paste until it is fragrant and begins to darken. Add the brandy and cook, stirring to scrape the brown bits from the bottom of the pot, until the brandy has evaporated. Pour the reserved wine marinade into the pot.
Add the chicken and any accumulated juices from the plate back to the pot and sprinkle the thyme over top. Add black pepper and bacon and cover the pot, turn the heat to low, and simmer for 40 minutes.
Meanwhile, pour 2 tablespoons of the butter into a large skillet. Add the mushrooms and sauté over medium-high heat until brown, about 5 minutes. Set aside.
In the same skillet and another 2 tablespoons of butter, add the pearl onions and two tablespoons of sugar and sauté over medium-high heat for about 6 minutes. Add mushrooms to the skillet with onions and cook for another 1 minute.
Add the pearl onions and mushrooms to the pot with the chicken and cook for 10-15 minutes more.
In a small bowl mix together butter and flour to make the beurre manie. Uncover the pot, remove the chicken from the pot then add the beurre manie. Stir it into the sauce and continue to cook until sauce starts to thicken. Season to taste with salt and pepper if necessary.
Add the chicken back into the pot and cook for another 1 minute. Serve hot.
