Generously season the short ribs with salt and pepper. In a large mixing bowl, whisk together the zinfandel, sugar, garlic, fresh thyme and a pinch of salt. Marinate the short ribs in the wine mixture for 12 hours in the refrigerator.
Pour 3 ounces canola oil into a Dutch oven over high heat. Remove the short ribs from the wine and allow the beef to rest for several minutes and come to room temperature. Reserve marinade.
Once the meat has rested, place in the hot pan. Stir and turn the meat often, carefully allowing each piece to brown on each side before removing from the pan. When browned (will take several minutes per side), remove the beef from the pan and add the onions, carrots, and celery. Stir constantly and allow the onions to cook until mahogany in color, about 10 minutes; if onions are browning too quickly, reduce to medium heat. Add the short ribs back to the pot along with the reserved wine marinade. Allow the wine to come to a boil before reducing the heat to a simmer, skimming foam and fat from the surface of the liquid. After simmering for several minutes, add remaining ingredients and allow to simmer uncovered until the meat is fork tender and nearly falling off the bone, roughly 5 hours.
Once the beef has cooked, transfer short ribs to a dish and cover. Reduce the pan liquids until they coat the back of the spoon, simmering about 30 minutes. Strain the braising liquid and return the short ribs to the liquid. Season the short ribs and braising liquid with salt and pepper to taste. Reserve for later use.
This may all be done up to 3-4 days in advance. Reheat in oven or microwave until meat is at least 160 degrees Fahrenheit.