To prepare stuffing & chicken: Combine spinach and breadcrumbs in a medium bowl with chicken livers (if using), Parmesan, egg, fennel fronds (if using), 2 tablespoons shallot, 1 tablespoon garlic, thyme, 1/2 teaspoon pepper and 1/4 teaspoon salt until well blended. Cover and refrigerate for at least 30 minutes or up to 1 day. Place a chicken thigh skinned-side down on a work surface. Fill the thigh with 2 to 3 tablespoons of the stuffing, first filling the area (or pocket) left by the bone and placing the rest in the center of the thigh. Roll the thigh closed and secure with 2 pieces of kitchen string. Repeat with the remaining thighs and stuffing. (You may leftover stuffing.) Season with the remaining 1/4 teaspoon pepper and salt. Heat oil in a large, heavy, high-sided skillet or Dutch oven over medium-high heat. Reduce heat to medium and add half the thighs, seam-side down. Cook, turning 2 or 3 times, until brown on all sides, 7 to 10 minutes total. Transfer to a clean plate and repeat with the remaining thighs. To prepare sauce: Add onion, carrot, fennel, 1/4 cup shallot and 2 tablespoons garlic to the pan. Cover and cook, stirring occasionally, until the vegetables are soft and beginning to brown, about 5 minutes. Add wine and scrape up any browned bits; bring to a boil over medium heat and continue to boil until the liquid is reduced by about half, 6 to 8 minutes. Stir in broth, tomatoes, basil, thyme and the chicken thighs. Bring to a boil over high heat; reduce heat to a simmer and cook, uncovered and turning the thighs occasionally, until cooked through and tender, 35 to 40 minutes. Remove the thighs with a slotted spoon; tent with foil to keep warm. Simmer the sauce further to thicken it, if desired, or thin with a little broth or water if it’s too thick. Season with 1/2 teaspoon pepper and 1/4 teaspoon salt. Serve the chicken with the sauce.