Rub some salt and pepper on the pork shoulder (or beef if you're using that).
In a dutch oven heat the oil over medium high heat. Sear the pork shoulder on all sides until it is browned. Remove the pork and set aside for now.
Add the cumin seeds to the pan and toast in the hot oil until fragrant. Add the chopped onions and saute until lightly browned on the edges. Then add the garlic and chopped chipotle peppers and saute until fragrant, about 30 seconds. Add the whole can of tomatoes including the liquid, bay leaves, dried oregano, cloves, chicken stock or some water and scrape up the browned bits on the bottom of the pan. Add the pork back to the pan and bring the contents up to a boil then lower to a bare simmer. Braise until the pork is fall apart tender, about 3 - 4 hours (or 6 hours in a slow cooker). You can braise on the stovetop on a low heat setting, in the oven at 325 deg F, or in a slow cooker.
The meat is done when it is fall apart tender. Try your best to remove it in one piece and set aside. Remove the cloves, bay leaves, and oregano sprig (if you used the sprigs) from the braising liquid. Then in a food processor or blender puree into a sauce. If the sauce is too thin, simmer it on the stovetop until it has reduced a little. Meanwhile, using two forks, shred the pork shoulder. Return the shredded meat to the simmering sauce. Let it heat through and soak up all the flavor and juices.