uncooked bone-in beef short ribs (about 3 lbs.), trimmed of, kosher salt, divided, black pepper, divided 2 tablespoon olive oil, divid, onion, peeled, chopped, Marsala wine, beef broth, brown sugar, garlic, peeled, minced, fresh thyme, minced, divided, carrots, peeled, cut in 1-inch pieces, parsnips, peeled, cut in 1-inch pieces, pearl onions