Season the short ribs with 1 tablespoon thyme and the cracked black pepper. Use your hands to coat the meat well. Cover, and refrigerate overnight.

Take the short ribs out of the refrigerator an hour before cooking, to come to room temperature. After 30 minutes, season them generously on all sides with salt.

Preheat the oven to 425 degrees F.

Toss the pearl onions with 2 tablespoons olive oil, 1 teaspoon thyme, ¾ teaspoons salt, and a pinch of pepper. Spread them on a baking sheet and roast them about 15 minutes, until tender. When they have cooled, slip off the skins with your fingers and set aside. Turn the oven down to 325 degrees F.

Heat a large Dutch oven over high heat for 3 minutes. Pour in 3 tablespoons olive oil, and wait a minute or two, until the pan is very hot and almost smoking. Place the short ribs in the pan, and sear until they are nicely browned on all three meaty sides. Transfer them to a plate to rest.

Turn the heat down to medium, and add the onion, carrot, celery, thyme springs, and bay leaves. Cook 6 to 8 minutes, until the vegetables just begin to caramelize. Add the balsamic vinegar, port, and red wine. Turn the heat up to high, and reduce the liquid by half.

Add the stock and bring to a boil. Arrange ribs in the pot, lying flat, bones standing up, in one layer. Cover tightly with aluminum foil and a tight-fitting lid. Braise in the oven for about 3 hours.

To check the meat for doneness, remove the lid and foil. When the meat is done, it will yield easily to a knife. Let the ribs rest 10 minutes in their juices, and then transfer them to a baking sheet.

Turn the oven up to 400 degrees F. Place the short ribs in the oven for 10 to 15 minutes to brown.

Strain the broth into a saucepan, pressing down on the vegetables to extract all the juices. Skim the fat from the sauce and reduce it over medium-high heat to thicken slightly.

Heat a large sauté pan over high heat for 2 minutes. Tear the Swiss chard into large pieces. Add 3 tablespoons olive oil to the pan, and stir in the cooked pearl onions. Add half the Swiss chard, and cook for a minute or two. Add a splash of water and the second half of the greens. Season with salt and pepper. Cook until the greens are tender.

Place the Swiss chard on a large warm platter, and arrange the short ribs on top. Spoon lots of braising juices over the ribs. Serve the potato puree and horseradish cream on the side.