Heat 3 tablespoons of oil in a wide 10- to 12-quart pot over medium-high heat. When it begins to smoke, add the beef and brown very well on at least two sides, 4-6 minutes per side. Add 5 cups of water and scrape the bottom of the pot to loosen any browned bits. Add the onion wedges, garlic, bay leaves, and 2 teaspoons salt and bring just to a simmer. Skim the liquid and reduce the heat to medium-low and partially cover; gently simmer the mixture until tender, about 2 hours, stirring occasionally. Let the beef sit in its liquid, uncovered, until cool enough to handle.
Meanwhile, preheat the broiler. Lay the tomatoes on a rimmed baking sheet double-lined with foil. Drizzle with a few tablespoons of oil. Broil on both sides (drizzling the second side with oil as well) until the tomatoes have concentrated and are blackened in spots, 4 to 8 minutes per side. Let cool and transfer along with any juices to the bowl of a blender.
Warm 2 teaspoons of oil in a small skillet over medium heat. Toast the almonds until pale golden, tossing and stirring regularly. Transfer to a plate to cool.
When the meat is cool enough to handle, remove it from the liquid and transfer to a bowl. Break the beef into small, bite-size pieces with your fingers and set aside. Discard the bay leaves from the cooking liquid and transfer 1/2 cup or so of the cooking liquid and half of the onion and garlic pieces from the pot to the bowl of the blender. Add the chiles and a bit of the adobo sauce, the cinnamon, cloves, and black pepper. Process to form a nearly smooth thick paste, with no large bits of chile remaining, scraping the sides of the bowl and adding a bit more liquid as needed. Reserve 1 cup of the braising liquid (refrigerate the remaining liquid for another use).
Return the chile-tomato paste, beef, reserved 1 cup of braising liquid, and the raisins to the pot. Simmer the mixture over medium-low heat until the meat is coated in a thick, barely fluid sauce, 15 to 20 minutes, stirring occasionally. Stir in the reserved almonds and let the beef sit off the heat for a few minutes. Add salt to taste and serve in warm tortillas (2 to 3 tablespoons of filling per tortilla) with salsas, chopped white onion, cilantro, lime wedges, and Cotija cheese, if you like. The mixture can be made up to 2 days ahead and reheated on the stovetop with a half cup or so of water, or partially covered in a microwave.
