Preheat oven to 325ºF/165ºC
Tie thyme and rosemary sprigs together with kitchen twine and set aside.
Place short ribs on a large plate or parchment-covered sheet pan and pat dry with paper towels. Season with 2 teaspoons of salt, turning the ribs to coat them on all sides.
Heat 2 tablespoons oil in pot over medium-high heat until hot (starting to wrinkle) and sear the ribs in 2 or 3 batches so as not to crowd the pan, browning them on all sides, about 5 minutes per batch, and transfer them to a large bowl.
Remove the pot from the heat and pour off all the fat. Set the pot over medium heat and add 1 tablespoon oil. Add the shallots and carrots and cook, stirring occasionally, for 6-8 minutes, until the vegetables start to brown. Add the garlic and cook, stirring, for 1 minute.
Add the wine and scrape the bottom of the pot with a wooden spoon to mix in any flavorful bits stuck on the bottom. When the wine comes to a boil, lower the heat and simmer until the wine has almost evaporated, about 8 minutes.
Add the tomatoes, thyme and rosemary, orange zest, bay leaves, cinnamon, star anise, black pepper, and 1 teaspoon salt. Stir to combine.
Return beef to the pot, along with any accumulated juices, sinking the ribs down into the sauce and spooning some sauce over them. When the sauce returns to a simmer, cover the pot, transfer it to the oven and cook for 2 hours, undisturbed.
Remove pot from oven. Lift the ribs from the sauce with tongs and place them in a large bowl. Set them aside.
Degrease (de-fat) the sauce by using a pot holder to carefully tilt the pot a little until the clear fat flows to one side in a pool. Use a tablespoon to scoop out as much of the fat as you can easily remove, without taking any of the sauce. (see notes)
Add the 1 ¼ cups water and the squash to the pot and bring to a simmer. Cover and cook gently for 20-25 minutes, until the squash is tender.
While the squash simmers, tend to the meat, which should be tender and practically falling off the bones. Pull the bones out and cut the meat into bite-sized pieces.
When the squash is tender, remove the bay leaves, herb stems, cinnamon sticks and star anise from the stew. Return the meat to the pot and simmer for a few minutes until the meat is heated through. Taste the stew and add additional salt and pepper, if needed.
Mix the parsley with the lemon zest and sprinkle it over the stew and serve. Or ladle the stew into individual serving bowls and garnish each one with parsley and lemon zest.