1. Make the rabbit: Preheat oven to 350°. Season the rabbit pieces with salt and pepper place in a large bowl with the crème fraîche. Cover and marinate in the refrigerator for at least 2 hours or overnight.
2. Remove the rabbit from the refrigerator an hour before cooking to bring the meat to room temperature.
3. In a large Dutch oven over medium heat, add the olive oil. When the oil is hot, add the bacon and cook, stirring occasionally, until the fat just begins to render but the bacon is not yet crisp, 5 to 7 minutes. Add the shallots, garlic and shinko and cook, stirring often, until the shallots have softened and the flavors have melded together, 12 to 15 minutes.
4. Place the thyme, bay leaves, orange peel and black peppercorn in the center of a triple layer of cheesecloth. Gather up the ends and tie using kitchen twine to form a bouquet garni. Add the bouquet garni to the pot and and cook for 2 to 3 minutes until fragrant. Add the white wine and reduce by half, 2 to 3 minutes. Add the reserved rabbit with the crème fraiche and the water and bring to a simmer. Cover the dish and bake for 50 minutes to 1 hour, rotating the pot every 20 minutes. Transfer the rabbit pieces to a clean plate; reserve the pot and cooking liquid.
5. Remove and discard the bouquet garni. Bring the cooking liquid to a boil, reduce the heat and simmer until the liquid thickens and becomes velvety, 20 to 30 minutes. Return rabbit to the pot and toss to coat until heated through.
6. Meanwhile, in a small bowl, make the gremolata: Combine the parsley, lemon zest and red pepper flakes.
7. To serve, arrange the rabbit pieces on a platter and garnish with the gremolata.