Season chicken pieces on all sides using 1 teaspoon of each salt and black pepper. Dredge the chicken pieces in the flour to coat lightly.
In a large 12 inch heavy sauté pan, heat the olive oil over medium-high heat. Add the chicken thighs to the pan and sauté just until brown, about 5 minutes per side. Fry in batches, if needed. Remove to a platter and set aside.
To the pan add the onion, green bell pepper, red bell pepper and mushrooms. Cook over medium heat until tender, about 5-8 minutes. Add garlic, cook for 1 minute longer.
Add wine, scraping any brown bits from the bottom of the pan.
Next, add the tomatoes (don't drain), stock, capers, Italian seasoning, reserved salt, oregano OR dry Italian seasoning and crushed red pepper flakes. Return the chicken pieces to the pan and turn them to coat in the sauce.
Bring the sauce to a gentle simmer. Simmer for 20-30 minutes with the lid offset or until the chicken has reached an internal temperature of 165°F and juices run clear.
To Thicken the Sauce: (Optional) If desired, remove chicken to a platter. Increase heat to medium. Mix in tomato paste one tablespoon at a time mixing until it's completely incorporated and melted. Repeat until your desired thickness is reached. Likewise, you can thin the sauce by adding more stock.
Serve chicken drizzled with sauce, garnished with fresh parsley or fresh basil.