Preheat the oven to 400 degrees F.
Put the pancetta and 1 tablespoon of the oil in a large skillet and cook over medium heat until the pancetta crisps, about 3 minutes. Remove pancetta with a slotted spoon, reserve the oil in the pan. Season the chicken thighs with salt and pepper, and add skinned side down to the pan, and brown, in batches if needed, over high heat, about 4 minutes per side. Transfer the chicken to a plate.
Add a tablespoon of oil and the mushrooms to the skillet and cook, without stirring until beginning to brown, 2 to 3 minutes. Shake pan and continue to cook the mushrooms until evenly golden brown, about 3 minutes more. Add the onion, garlic, marjoram, and pepper flakes; cook stirring and scraping the bottom of the pan with a wooden spoon until fragrant. Crush the tomatoes through your fingers and add to the pot; cook until brick red. Stir in the tomato juices. Bring the sauce to a simmer. Return the chicken and pancetta to the pan and cook it in the oven until the meat is cooked through and tender about 30 minutes more.
Divide the chicken evenly among 4 plates, cover loosely with foil. With a large spoon or ladle, skim any fat off the surface of the sauce and discard. Stir the cheese and parsley into the sauce, and season with salt and pepper, to taste. Pour the sauce over the chicken and serve.
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