Season the short ribs generously with salt and pepper. Heat 2 tablespoons oil over medium-high heat in a Dutch oven or heavy skillet. Brown the short ribs in batches until they are nicely seared, about 5 minutes per side. Remove the ribs and let aside on a plate.
Add the onion and pepper to the pot and cook, stirring occasionally until the vegetables are softened, about 5 minutes. Add the garlic, chipotles, and cumin and cook, stirring for another 60 seconds. Pour the tequila into the pan and scrape any browned bits off the bottom of the pot. Continue to cook the mixture until most of the liquid has evaporated. Transfer the mixture to the Instant Pot, add the ribs and beef broth and cook on high for 50 minutes then let the pressure release naturally for 15 minutes. Remove the ribs to a plate and let cool until cool enough to handle. Strain the vegetables through a fine mesh strainer into a large liquid measuring cup. Place the measuring cup in the freezer while the short ribs cool, about 15-20 minutes. Put the vegetables into a large mixing bowl.
Preheat oven to 375 degrees and lightly grease a 9 by 12 (or similar) baking pan.
Shred the short ribs, removing any fat or connective tissue, into the bowl with the vegetables and mix.
Spoon off as much of the at that has risen to the top of the cooking liquid. Pour 1 cup of the liquid into a medium mixing bowl, add the enchilada sauce, and stir to combine.
Pour enough oil into a large skillet to come up ¼ - ½ inch. Line a plate or baking sheet with paper towels. Heat the oil over medium-high heat. Cut the tortillas in half and fry them for about 10-20 seconds per side or until softened and just starting to lightly brown. Drain on the paper towels.
Pour 1½ cups of the enchilada sauce mixture into the bottom of the prepared pan. Place a layer of tortillas on the bottom of the pan. Top with half the meat mixture, spreading into an even layer, and spread a layer of 2 cups cheese on top. Repeat the layers then top with 1½ cups of enchilada sauce. Top with a layer of tortillas, the rest of the sauce, the last 2 cups of Mexican cheese and crumble the cotija cheese over the top.
Cover the dish with foil and bake for 15 minutes. Remove the foil, bake for another 10 minutes and remove from the oven. Let cool for about 5 minutes, garnish with cilantro and serve.