Generously salt and pepper all sides of the short ribs. (Use more salt than you think) Heat oil in a heavy bottom Dutch oven over medium high heat. When the oil is hot,add the ribs and brown all sides of the ribs – be patient, it takes time and this step is quite important. If splattering, cover partially with a lid. You want a nice deep color on all sides. This is crucial! Be careful not to overcrowd ( you may want to do in batches). Once they are nice and brown, remove and set aside.
In the same pot, turn heat to down medium and add onions and whole garlic, stirring constantly until golden brown and just tender about 3-4 minutes. Add cumin, cinnamon stick, allspice, oregano and bay leaves, and stir for 1-2 minutes. Add chilies, beer, stock, and brown sugar and give a stir, and place the short ribs in the liquid with the bone sticking strait up. Liquid will just come to the top of the ribs.
Turn heat to high, bring to a boil. Cover with a tight fitting lid …or with two-three layers of foil, creating a tight seal. Place in the middle of the hot oven and bake for 3 hours, without opening the lid.
In the mean time, slice one large onion into ⅓ inch thick rings and sauté in a little oil on medium high for 5 minutes, turn heat to low and sauté until caramelized and golden, about 10 more minutes.
You could also make pico de gallo or pickled radishes ( optional) … see link above.
After 3 hours, the meat will be fork tender and flavorful. Leave the meat in the braising liquid until ready to serve. When ready, remove ribs from the liquid. Skim the fat, from the pot. Using a fork, or tongs, separate meat from bone and fatty parts and set meat aside. Taste the meat for salt, adding more if necessary. Fish out some of the flavorful chili peppers from the liquid and toss with the meat along with a few tablespoons of the juices left in the pot. The little bits of cumin seed are good too. Remember the meat will dry out quickly once removed from the cooking liquid, so if not serving right away, keep the ribs in the liquid.
Place cheese on tortillas, then place directly on the racks inside a 350 F oven, until melted. Remove from the oven, and place some of the meat, caramelized onion, cilantro and hot sauce inside the tortilla. Serve.