Place pork butt, yellow onions, cumin, bay leaves, Mexican oregano, salt, black peppercorns and cayenne in a large saucepan and cover with water by 1-inch. Bring to a boil.
Lower the heat to medium-low and simmer until tender, about 45 minutes, skimming the surface to remove any scum that forms. Drain in a colander.
Shred the drained pork and return to the pot. Add the Chile Verde and stir well. Bring to a simmer over medium-low heat, and cook until heated through. Serve hot with tortillas and other desired condiments.
Roast the peppers by placing them on an open gas flame, turning them frequently with tongs until all sides are charred black, about 7 to 10 minutes. (Alternately, the peppers can be roasted under a broiler, or on top of a gas or charcoal grill.) Place the blackened peppers in a plastic or paper bag, and let rest until cool enough to handle, about 15 minutes. Peel the peppers, and remove the seeds and the stems. Chop the peppers and set aside.
In a large saucepan, heat the oil over medium-high heat. Add the onions and cook, stirring, until tender, about 3 minutes. Add the garlic, jalapenos, oregano, salt, and cumin, and cook, stirring, for 1 minute. Add the flour and cook, stirring, without allowing to color, for 2 minutes. Add the chopped peppers, and stir well to combine. Add the chicken stock, stir well, and bring to a boil. Lower the heat to medium-low and simmer, stirring occasionally, for 30 minutes.
Remove the chile verde from the heat, add the cilantro, and adjust seasoning, to taste.