Preheat oven to 300 F. Pat short ribs very dry and liberally sprinkle with salt on all sides. Heat a large Dutch oven over medium heat. Once hot, add the olive oil. Once shimmering, add the short ribs, working in batches to not overcrowd the pan. Brown each side, then remove from the pot.
Lower heat to medium and add onions, leek, carrots and celery to the pot. Cook for a few minutes, stirring frequently until the vegetables are fully softened and golden. Add the garlic and cook 2-3 more minutes. Add tomato paste, and mix until fully incorporated and darkened in color.
Pour in the wine to deglaze, scraping any bits at the bottom of the pan. Add the broth, crushed tomatoes, parm rind, seasonings, salt and pepper and mix. Nestle the short ribs in the pot, topping with the rosemary and thyme. Bring to a boil then cover and set in the middle rack of the oven for about 2 ½-3 hours, until the short ribs shred easily with a fork. Uncover the pot and cook for another 45 minutes - 1 hour until the sauce has reduced a bit.
In the meantime, make the gremolata. Add all the ingredients to a small bowl and mix to combine. Set aside to allow the flavors to meld.
Remove pot from oven and discard the bay leaves, thyme, rosemary, bones and parm rind. Transfer meat to a large bowl and shred into fine pieces using two forks.
Optional if you like a smoother sauce: use an immersion blender to carefully blend the remaining sauce in the pot. I did half to keep some of the texture. Add shredded meat back to the sauce and mix to combine. Season with more salt and pepper if needed.
Boil 1 lb of pasta, liberally salted, 2 minutes shy of al dente. Drain, and add about 2 ½ cups of the ragu along with 1 cup of pasta water to the pasta. Gently mix, cooking until the pasta has reached al dente. Add more ragu if you like it even saucier or more pasta water if the sauce needs to be thinned.
Serve with ample shredded pecorino and the gremolata to top!