In a blender, combine the orange juice, lime juice, white vinegar, achiote paste, garlic, oregano, cumin, cinnamon, salt, and black pepper. Blend until smooth.
In a large bowl, combine the pork shoulder chunks and the marinade. Mix until the pork is evenly coated. Cover and refrigerate for at least 2 hours, or overnight for best results.
Preheat oven to 325°F (163°C).
In a large Dutch oven or casserole dish, layer the sliced onions and bay leaves. Add the marinated pork and any remaining marinade. Pour in 2 cups of water.
Cover the dish with banana leaves (optional) and then with a lid. If using a casserole dish without a lid, cover tightly with foil.
Bake in the preheated oven for 3 to 4 hours, or until the pork is tender and falls apart easily with a fork.
Remove from the oven and discard the banana leaves (if used) and bay leaves.
Shred the pork with a fork and mix it with the cooking juices.