In a wide stockpot or Dutch oven, combine the short ribs, soy sauce, vinegar, garlic, lemongrass, ginger, brown sugar, water, green onion bottoms, crushed red pepper, and 2 tablespoons of the orange juice. Make sure that the stockpot is deep enough so that the short ribs are submerged in the liquid.
Bake the short ribs, covered, for about 3 hours, or until the meat is tender and falling off the bones. Remove the short ribs from the braising liquid and cover to keep warm. Increase the oven temperature to 425 degrees F.
Drain the fat off of the cooking liquid and discard. Place the remaining braising juices in a medium saucepan with 1/4 cup of the hoisin sauce and bring to a boil over medium-high heat. Reduce the liquid until only about 1 1/4 cups remain. Strain through a fine-meshed strainer, discarding the solids. Stir in the remaining 2 tablespoons of orange juice and the lemon juice.
Return the short ribs and the reduced sauce to the stockpot or Dutch oven, coating the short ribs well with the sauce. Bake for 10 minutes, until the short ribs are heated through and slightly glazed. Serve hot over jasmine rice. Season each portion with the orange zest and garnish with the green onions if desired.