Sprinkle the chicken on all sides with salt and pepper. Place the chicken pieces, a few at a time, into a large (gallon-size) ziplock bag along with the flour. Shake to coat all of the pieces of the chicken. Remove the chicken from the bag and place on a metal rack.
Add 2 tablespoons of water to a large saute pan over medium heat along with the bacon. Cover and cook until the water is gone, and then continue to cook until the bacon is crispy, approximately 8 to 10 minutes. Remove the bacon from the pan (but leave the fat) and set aside.
In the same pan, using the remaining fat, add one of the onions, sprinkle with salt and pepper, and saute until it begins to brown, approximately 8 to 10 minutes. Remove the onions and set aside. Next, brown the chicken pieces on each side until golden brown, working in batches if necessary to not overcrowd the pan. Transfer the chicken into a 7 to 8-quart dutch oven.
Add the mushrooms to the saute pan used for the bacon and onions, adding 1 tablespoon of butter and saute about 5 minutes, then set them aside with the onions and bacon.
Pour off any remaining fat and deglaze the pan with 1 cup of the wine. Pour this pan sauce into the dutch oven along with the chicken stock, tomato paste, the second onion, carrots, celery, garlic, thyme, and bay leaves. Add all of the remaining wine.
Place in a 325 degree oven and cook for 2 to 2 1/2 hours, or until the chicken is tender. Maintain a very gentle simmer and stir occasionally.
Once the chicken is done, remove it to a platter and cover with foil to keep it warm and moist. Then strain the pan sauce into a colander with a pot below it to catch all the liquid. Remove the carrots, onion, celery, thyme, garlic, and bay leaves. Return the sauce to the pot, place over medium heat, and reduce by 1/3. Depending on how much liquid you actually began with, this should take 20 to 45 minutes.
Once the sauce has thickened, add the reserved onions, mushrooms, and bacon, and cook for another 15 minutes or until the heated through. Taste and adjust seasoning if necessary, remove from the heat, add the chicken and serve over mashed potatoes.
(Note: If the sauce isn’t thickening, try adding equal parts butter and flour kneaded together (like a roux). Start with 1 tablespoon of each. Whisk it into the sauce for 4 to 5 minutes and repeat if necessary.)