Preheat oven to 350˚F. Season the short ribs on all sides with kosher salt and black pepper.
In a cast iron skillet, add the 3 tablespoons bacon fat or olive oil and melt completely. Add the short ribs and brown completely on all sides. Set aside to drain on a paper towel and let rest as the next stage is prepared.
Deglaze the skillet with white wine, scrapping up the little browned bits. Turn off the heat and leave until next step. Set aside.
In a large Dutch oven add 1 tbsp of oil to the pan and add the onion, carrots and celery (a mirepoix). Let sweat for a few minutes and add the garlic and red pepper flakes. Next add the flour and stir to cook out the flour as a roux base for the sauce, a minute or two.
Next, add the water and stir to incorporate completely. Add the deglazed white wine drippings from the skillet.
Next add the potatoes and place each short rib in the pot, nestled in between the vegetables. Push them down and make sure there is enough liquid to cover. Add the bay leaves, oregano and wrapping the thyme into a bundle, toss in the pot. Use 2 teaspoons of dried thyme if fresh is not available. Add beef broth or more if needed to cover all.
Bring to a boil and remove from heat. Cover with the lid and place the Dutch oven or casserole dish in the oven to bake for 3 hours.
Remove the braised short ribs from the vegetable mixture and keep warm. Let the mixture cook down, lid removed, for 10 minutes to condense the sauce if needed. Season if needed. Plate ribs and pour vegetables and sauce mixture over all. Garnish with parsley.