Place a large pot of water over high heat and bring up to a boil for the pierogies.
Meanwhile, place a large, deep skillet over medium-high heat with 2 teaspoons of the olive oil. Add the bacon and cook until just brown and crisp, 3-4 minutes. Season the chicken with salt and pepper, add to the skillet with the bacon, and brown all sides, 7-8 minutes. Add the onions, carrots, garlic, paprika, cumin, marjoram or oregano, and bay leaf and cook for 5-6 minutes, until the veggies are just tender.
Make a well in the middle of the pan and add 2 tablespoons olive oil. Add the flour to the olive oil and mix to form a paste. Add the wine (or 1/2 cup chicken broth), scraping up all of the brown bits on the bottom of the pan. Add 2 cups chicken stock and the tomatoes and cook for about 20 minutes, until the stew has thickened. Stir in the sour cream and remove from the heat.
While the stew is cooking, cook the pierogies in boiling water according to the package directions. Heat a medium skillet over medium-high heat, add the butter and cook until the butter turns slightly brown and gives off a nutty aroma. Drain the cooked pierogies, add them to the pan, and cook until slightly browned on both sides, about 2 minutes per side. Add the chives and turn the pierogies to coat.
Serve the stew in large bowls, sprinkled with lemon zest and parsley. Arrange 2-3 pierogies on top of each bowl of stew.