Start by combining miso paste, soy sauce, brown sugar, rice vinegar, sesame oil, garlic, ginger, and water in a bowl. Mix until smooth and well combined. This marinade should be thick but pourable. Taste and adjust seasoning if needed.
Place the short ribs in a large bowl or zip-top bag and coat them evenly with the marinade. Make sure every piece is well covered. Let them marinate for at least 2 hours, but overnight is best for deeper flavor.
Heat a Dutch oven over medium-high heat and add a bit of oil. Sear the ribs on all sides until nicely browned. This step locks in flavor and creates a rich crust that enhances the final dish.
Pour the remaining marinade over the ribs and cover the pot. Reduce heat to low and let it cook gently for 2.5 to 3 hours. The ribs should become very tender and almost fall apart when done.
While the ribs cook, blend cilantro, olive oil, lime juice, garlic, jalapeño, and salt until smooth. Taste and adjust seasoning. The salsa should be fresh, tangy, and slightly spicy.
Once the ribs are done, let them rest for a few minutes. Spoon the cilantro salsa over the ribs just before serving. The contrast of rich meat and fresh sauce makes every bite exciting.