Preheat the oven to 325° F.
Start by preparing the short ribs. Pat the short ribs dry with paper towel and season all over with salt and pepper. Heat 1 tablespoon of avocado oil in a medium Dutch oven or sauté pan over medium-high heat. When the oil is hot and shimmering, add the short ribs and brown the meat on all sides (this should take about 10 minutes). Once browned, transfer the short ribs to a plate. Reduce the heat to medium-low and add the remaining tablespoon of avocado oil. Add the onion and garlic to the pan and cook for about 3 minutes or until the onion is soft and translucent. (Be careful not to burn the garlic! Keep things moving around the pan and lower the heat if necessary.) Add the paprika and cook for 1 minute just to toast the spice. Stir in the tomato paste, chipotle pepper, adobo sauce, honey, apple cider vinegar, soy sauce, and 1½ cups of the beef broth. Bring to a boil then lower to a simmer and add the short ribs. Cover the pan with a lid and transfer to the oven and cook for 1 hour. Turn the short ribs over and cook for 1 hour more until the short ribs are very tender and easy to break down with a fork. (If the short ribs aren’t tender after 2 hours, allow them to cook for another 15 to 30 minutes.)
Meanwhile, combine all the ingredients for the doctored refried beans in a bowl. Cover and set aside.
Make the cherry tomato pico de gallo. Combine all the ingredients in a mixing bowl. Season with salt, pepper, and extra lime juice to taste. Cover and set aside. (Feel free to refrigerate the pico if you’d like.)
Moving on to the guacamole! Cut each avocado in half lengthwise and remove the pit.Scoop the flesh into a small bowl. Immediately add the lemon and lime juice, and a pinch of salt and mash with a fork until relatively smooth. Stir in the cilantro and onion and season with extra salt and black pepper to taste. Press plastic wrap onto the surface until ready to use.
When the short ribs are tender, transfer the short ribs to a cutting board and shred the meat with two forks. I like to leave some larger chunks intact, but you do you. Return the shredded meat to the sauce. (The sauce should be quite thick—a true BBQ sauce consistency—but if it seems very thin, simmer for 5-10 minutes, uncovered, to thicken it up a bit.)
Increase the oven temperature to 375° F. Line a large, rimmed baking sheet with parchment for easy cleanup.
Nacho assembly time! Arrange the tortilla chips in an even layer on the baking sheet. Dollop the baked beans all over the chips. (You can leave them as dollops or spread them out a bit.) Sprinkle half the cheese over the chips. Add the warm BBQ short ribs in a relatively even layer and sprinkle with the remaining cheese.
Bake for about 8 to 12 minutes or until the cheese is fully melted. (Keep an eye on it!)
Top the nachos with cherry tomato pico de gallo (I like to use a slotted spoon to avoid adding excess liquid to the nachos), guacamole, pickled jalapeños and cilantro (if using). Serve immediately.