Separate the red onions into rings and place in a small plastic container. Dress with the lime juice and season with salt and pepper. Cover and store in the refrigerator.
Place the ancho chiles in a pot and cover with the chicken stock. Turn on the heat and warm the stock to reconstitute the chiles, 10 minutes or so.
Meanwhile, in a large Dutch oven, toast the almonds and peanuts over medium heat until browned. Transfer the nuts to a food processor. Reserve the pot. Add the ancho chiles with the stock to the food processor along with the cocoa powder, cloves, garlic, yellow onions and raisins. Season with salt and pepper. Puree until smooth. (You may need to do this in two batches.)
Pat the pork dry and heat a thin layer of oil in the Dutch oven over medium-high heat. Sprinkle the pork with salt and pepper, then brown in two batches, adding more oil between batches as needed. Return all the pork to the pot and pour the ancho sauce over it. Bring the mixture to a boil and add the bay leaves and cinnamon stick. Reduce the heat to a simmer and cook until the pork is very tender, 1 hour 15 minutes to 1 1/2 hours (depending on how large you cubed the meat).
Warm or char the tortillas. Serve the stew with the lime-pickled onions, crumbled cheese and the tortillas.
Cook's Note: If you are not serving the pork immediately, cool and store it in the refrigerator. Reheat over medium heat.