Make the kelp stock (if using)
Pour the water into a large bowl. Wipe the kelp with a moist, clean kitchen towel to remove any sand or impurities. Do not wipe off the white mannite powder. Add the kelp to the bowl (you may need to break the kelp into pieces to fit into the bowl). Cover the bowl with plastic wrap and refrigerate overnight.
Remove the kelp from the water. On the ends of the swollen kelp you will see some oozing of a slimy liquid. This is a healthful, dietary fiber and a portion of it has already been dissolved in the stock.
If a greenish slimy substance is leaking out into the water and is clouding the stock, it is a sign that you are using poor-quality kelp, as stock prepared from good-quality kelp will be clear in appearance. If necessary, strain the stock through a sieve lined with a moist, sturdy paper towel to remove any impurities.
Make the short ribs
In a large bowl, combine 6 Tbs. of the soy sauce, the honey, Worcestershire sauce, and red pepper flakes. Add the short ribs to the sauce and marinate for 2 hours.
Heat the oven to 325°F. Bring a medium pot of water to a boil. Remove the short ribs from the marinade and wipe them with paper towels, reserving the marinade. Place the canola oil in a large skillet over medium heat and add half the meat. Cook the ribs until all sides are golden brown, 4 to 6 minutes total. Transfer the browned short ribs to a sieve, and lower the ribs into the boiling water. Quickly swish the ribs in the water and remove them, discarding the water after both batches of ribs have been cooked and washed.
Combine the sake and stock in a large pot over medium heat and bring it to a simmer. Add the sugar and the ribs (in a single layer) and bring the mixture to a gentle boil. Cover the pot with a lid, transfer it to the oven, and cook the short ribs for 1 hour.
Cut the Swiss chard in half lengthwise along the center of the stems, and then crosswise into 2-inch slices. Bring a medium pot of salted water to a boil. Add the Swiss chard and cook for 1 minute. With a slotted spoon, transfer the Swiss chard to a colander to drain and air-dry. Add the cipollini onions to the boiling water and cook for 2 minutes. With a slotted spoon, transfer the onions to the colander with the Swiss chard.
Remove the pot of short ribs from the oven and transfer it to the stovetop. Add the reserved marinade to the pot and cook, covered, over medium-low heat for 15 minutes. Add the prunes and cipollini onions and cook for 15 minutes longer. Toward the end of the cooking time, taste the cooking liquid and, if desired, add the remaining 1 Tbs. soy sauce.
Remove the beef, prunes, and onions from the cooking liquid and place them in a bowl. Transfer the cooking liquid into a gravy separator to remove the excess fat. Return the cooking liquid to the pot (you will have about 2 cups) and add the vinegar. Cook the liquid over medium heat, uncovered, until it is reduced to two-thirds of its previous volume. Return the short rib, prunes, and onions to the pot, and add the Swiss chard and tomatoes. Cook the short ribs and vegetables, covered, over low heat for 5 minutes, or until the ribs and vegetables are heated through. Divide the meat and vegetables among dinner plates and pour the remaining cooking liquid over them. Serve the dish with crusty bread.
The kelp stock can be made 2 to 3 days ahead and refrigerated. By cooking and refrigerating this dish a day ahead of time, you can remove coagulated fat from the top of the meat broth and allow the flavors to mingle.
Serve the dish with some crusty bread to enjoy the sauce left on your plate.
Freeze unused kelp stock in 2-cup portions in small plastic containers for up to 2 months. To defrost frozen stock, place it in a small pan with a tight-fitting lid and cook over medium heat. Defrosting 2 cups of frozen stock this way takes about 5 minutes.