Preheat the oven to 325°F (160°C) or select a slow-cooker large enough for the ribs (a 5-quart or larger should work fine).
Season the short ribs quite generously with salt and pepper and let rest at room temperature.
Toast the cumin seeds in a dry skillet over medium heat, shaking the skillet occasionally to prevent scorching, until fragrant, 2 to 3 minutes. Immediately transfer the toasted spices to a spice grinder. Repeat with the coriander seeds. Grind until the spices turn into a fine powder. Dump the spices into a bowl, add the chili powder, paprika, salt, oregano, and sugar, and mix well.
Heat the oil in a Dutch oven over medium-high heat and sear the short ribs on all sides. Grab some tongs and transfer the ribs to a plate. Pour or spoon off some of the fat from the Dutch oven. Add the onions, garlic, and jalapeño to the fat that remains in the Dutch oven and cook, stirring and scraping the bottom, until the onions have softened and turned translucent. Lower the heat to medium-low. Add the spice mix and the chipotle in adobo and stir to combine. Add the canned tomatoes, tomato paste, and chocolate and use a wooden spoon or potato masher to break up the tomatoes. Return the ribs to the Dutch oven and gently toss to coat with the tomato and spice mixture.
To cook the short ribs in the oven:Arrange the short ribs in the Dutch oven in a single layer if possible, making sure each one is completely coated in the chili mixture. Pour enough water over top to just cover the short ribs, which should be 2 to 3 cups. Cover the Dutch oven securely, place in the preheated oven and cook for 3 or 4 hours, or until the ribs are completely tender and come off the bone. To cook the short ribs in a slow-cooker: Combine the ribs and sauce in the cooker. Rinse the Dutch oven with 2 cups water and pour this over the ribs. Set the slow-cooker to high for 3 hours, then turn down to low and cook for 2 to 4 hours more, until the ribs are completely tender and the meat comes off the bone. (If you want to cook the ribs while you are at work or out of the house, just set the slow-cooker to low and let it go for 8 to 10 hours.) When the short ribs are falling apart tender, grab some tongs and transfer the ribs to a plate until cool enough to handle. Then roll up your sleeves and discard the bones, membrane, and excess fat. Use 2 forks to shred the meat from the ribs. Return the shredded meat to the pot and stir to combine with the cooking sauce. If the sauce seems too thick, add water. If it’s too watery, you can add some masa harina dissolved in water and let it cook for about 5 minutes on high to thicken. Taste and adjust the seasoning by adding salt and pepper to taste. Serve in a large bowl, family style.