Remove the legs from the ducks and cut them into drumsticks and thighs. Remove the whole breasts on the bone. Split each breast down the center, then cut the breasts in half crosswise through the bones. Cut off and discard as much of the fat from the carcass as possible. Chop the back and neck bones into 2 or 3 pieces. Season the duck pieces and the reserved bones with salt and pepper.
Arrange the duck pieces and bones in a large, deep stainless steel roasting pan. Scatter the shallots, carrots, yellow onions, celery, peppercorns, juniper berries, bay leaves and 8 of the thyme sprigs on top. Pour the red wine over the meat and bones, cover with plastic wrap and refrigerate overnight. Turn the duck and bones in the marinade a few times.
Preheat the oven to 425°. Remove the duck pieces and bones from the marinade and pat dry. Strain the marinade in a colander; reserve the liquid and vegetables separately.
In a large skillet, heat 2 tablespoons of the olive oil. Add the drained vegetables and the head of garlic, season with salt and pepper and cook over high heat until the liquid evaporates and the vegetables start to brown. Reduce the heat to moderate and cook, stirring often, until the vegetables are evenly browned, about 8 minutes. Remove from the heat.
Return all of the duck to the casserole and add the tomato paste, stirring to coat. Sprinkle with the remaining 2 tablespoons of flour and stir to lightly brown the flour. Add the vegetables from the skillet and the reserved marinade and bring to a simmer. Cover with a round of parchment paper and a lid and braise in the oven for 1 1/4 hours; skim off the fat every 20 minutes or so.
Meanwhile, in a small saucepan, combine the cipolline onions with the chicken stock, sugar, 1 tablespoon of butter and the remaining thyme sprig and garlic clove. Season with salt and pepper. Cover with a round of parchment paper and simmer over low heat until the onions are tender, about 20 minutes. Remove from the heat.
Pour 2 inches of water into a small saucepan, add the bacon and bring to a boil; drain and pat dry.
In a large skillet, melt the remaining 1 tablespoon of butter over moderate heat. Add the bacon and cook, tossing, until lightly browned. Add the chanterelles, season with salt and pepper and cook, stirring occasionally, until tender, about 8 minutes; keep warm.
When the duck is done, transfer the drumsticks, thighs and breasts to a serving bowl. Strain the contents of the casserole through a coarse strainer set over a large bowl, pressing on the solids to extract as much liquid as possible; discard the solids. Skim the fat from the red wine sauce.