If you are using a whole chicken, break the chicken down by separating the wings, thighs, and breasts from the body. Further separate the drumsticks from the thighs by cutting through the joint and optionally cut the breast pieces into halves. Season all of the pieces of chicken with salt. Optionally refrigerate the chicken uncovered for at least an hour.
Cut the bacon in half lengthwise then rotate 90° and cut into ½ inch pieces widthwise. Heat a pan on medium heat and add the bacon to the pan. This will start rendering the fat out and browning the bacon. Stir frequently until it is sufficiently browned through and crispy and a layer of fond has been developed on the pan.
Remove the bacon and all but a tablespoon of bacon fat from the pan, leaving the fond. With the pan remaining on medium heat, add the chicken pieces to the pan, skin side down, beginning with the wings, thighs, and drumsticks. Sautee until the skin is a golden brown then turn and sautee until well browned on the second side. Remove the wings, thighs, and drumsticks from the pan and repeat with the chicken breasts. You should have a healthy fond built up on the base of the pan.
Add the onions, shallots, and mushrooms to the pan and season with salt. Stir or toss frequently to break up the fond on the bottom of the pan. The onions and shallots will begin to brown as they absorb the fond. Continue to cook until the onions and shallots just start to caramelize around the edges then stir the bacon back into the pan.
Add the butter and the flour and stir through, cooking for about a minute. Add the stock to the pan and stir through, scraping the pan to remove any remaining fond from the bottom and incorporate into the broth. Bring to the boil then reduce to a simmer.
Stir in the wine and bring back up to a gentle simmer before adding the chicken back to the pan. Add your thyme sprigs to the pan as well, submerging in the sauce. Maintain a very low simmer and then cover and allow to braise on the burner for 20-30 minutes, basting or flipping the chicken pieces halfway through.
Remove the lid and cook uncovered for another 15 minutes until the sauce has thickened slightly. Remove the thyme springs and season to taste.