To prepare the short ribs, in a Dutch oven over medium-high heat, warm the olive oil. Season the short ribs with the salt and pepper and dredge in the flour. Working in batches if needed, add the short ribs and cook, turning as needed, until well browned on all sides. Add the onions, celery and carrots, then stir in the tomato paste until blended. Gradually add the wine, stock and thyme. Bring to a boil, then reduce the heat to low, cover and simmer until the meat is very tender, about 3 hours. 

Transfer the short ribs to a bowl. When they are cool enough to handle, remove the meat from the bones; discard the bones, reserving the braising liquid for the sauce. It may be necessary to simmer the liquid and reduce it to achieve a richer finish in your sauce.

Meanwhile, prepare the pilaf: In a small pot over high heat, combine the farro, 4 cups of the water and 3 teaspoons of the salt. Bring to a boil, then cover, reduce the heat to a simmer and cook until the farro is tender, at least 55 minutes. After 30 to 35 minutes, check the water level—you may need to add a bit more water. Let the farro cool.

In another small pot over high heat, combine the quinoa, the remaining 4 cups water and 1 teaspoon salt, the cranberries and butter. Bring to a boil, then cover, reduce the heat to very low and simmer until tender, about 15 minutes. Let the quinoa cool.

In a large bowl, combine the farro and the quinoa-cranberry mixture, then add the thyme and mix well. Adjust the seasoning with salt, if needed.

To prepare the drizzle, in a bowl, stir together the crème fraîche and Gorgonzola until well blended. Season lightly to taste with salt, if desired. If you are preparing a lot of servings, transfer the crème fraîche–Gorgonzola mixture to a squeeze bottle.

To assemble each serving, put the farro-quinoa pilaf on the bottom, add a layer of braised short rib meat and top with the crème fraîche–Gorgonzola drizzle, then finish with a healthy spoonful of the reduced braising liquid.