To a large glass or non-reactive bowl, add the following ingredients: wine, red onion, garlic, rosemary, thyme, bay leaves, crushed fennel seeds, and red pepper flakes. Stir to combine all ingredients.
Add pork shoulder chunks to the bowl and turn the pork until each piece is covered. Then cover the bowl and place it in the refrigerator to marinate for at least 8 hours. While marinating, turn pork occasionally.
After the pork is done marinating, remove the bowl from the refrigerator and remove the pork from the marinade. Pat pork pieces dry with paper towels and set aside.
Separate the marinate liquid from the solids. Keep both liquids and solids, but discard the woody herb stems and bay leaves. Set aside.
In a large heavy-duty skillet or Dutch oven, heat olive oil over medium-high heat. Add pork and sear evenly on all sides until it is evenly browned. (This will take about 8-10 minutes.) Season to taste with salt and pepper.
Add the marinade solids and cook them until the onions are translucent and soft (about 10-12 minutes). Stir frequently.
Add the marinade liquids to the skillet and deglaze the pan by scraping the brown bits from the bottom. Continue to cook until the liquid has reduced to approximately one third of the original volume.
Add 1 cup chicken broth and tomatoes. Stir to combine. Cover and then reduce the heat to medium-low. Cook for 2 to 2 ½ hours and stir about every half hour. If needed, add more chicken broth while cooking.
When the pork has reached the point that it can be easily pulled apart with a fork, remove it from the heat. Let it rest in the warm juices for about 10-15 minutes. Serve immediately. Can be served over a bed of creamy polenta and garnished with chopped fresh parsley.