1. Put the sour orange juice, oregano, cumin, 1/2 teaspoon black pepper and the garlic in a large resealable plastic bag. Add the short ribs and toss with the marinade. Thinly slice one of the red onions and add it to the bag along with the bay leaves. Refrigerate 6 hours or up to overnight.
2. Preheat the oven to 325 degrees F.
3. Remove the short ribs from the marinade, lightly pat dry and sprinkle with salt and pepper. Remove the sliced onions from the marinade with a slotted spoon and set aside; discard the marinade.
4. Put the flour in a shallow bowl. Heat the oil in a large heavy-bottomed pan or Dutch oven over medium-high heat. Dredge the short ribs in the flour, shaking off any excess, and add to the pan. Cook until brown on all sides, about 3 minutes; remove to a plate. Add the chorizo to the pan and cook until some of the fat is rendered and the chorizo is slightly crisp, 3 minutes; remove to the plate with the short ribs.
5. Add the reserved marinated onions to the pan and cook until soft, about 3 minutes. Add the tomato paste and continue cooking for another 2 minutes. Add the sherry and cook until the liquid is reduced by half, 3 minutes. Quarter the remaining 2 red onions, leaving the root ends intact. Add the onions, short ribs and chorizo to the pan and pour in the chicken stock, making sure it reaches three-quarters of the way up the short ribs; add more stock if necessary.
6. Cover the pan, place in the oven and cook for 2 hours, making sure the liquid is gently bubbling. Adjust your oven temperature if necessary, checking the liquid every so often to make sure it is not boiling. After 2 hours, add the carrots and potatoes and continue to simmer until cooked through but not mushy, for an additional 30 to 40 minutes.
7. Transfer the short ribs to a large bowl and allow to cool slightly. Place the pan over medium-high heat and reduce the sauce until it begins to thicken, about 10 minutes. Trim the meat from the cooled ribs and cut into 1 1/2-inch chunks. Return the meat back to the pan, bringing the sauce back to a simmer and heating the meat through. Season with salt and pepper.
8. Ladle into serving bowls and garnish with chopped parsley.
Cook's Note: Sour (bitter) orange juice can be found in the Latin aisle of most supermarkets. You can easily substitute a combination of 1/2 cup orange juice and 1/2 cup lime juice.