Preheat the oven to 350°F (177°C), then char the grape tomatoes on a foil-lined baking sheet using a kitchen torch or broiler until the skins are blackened and the tomatoes have softened.
Let the tomatoes cool slightly, then rub off the skins with paper towels and either blend until smooth or leave them whole if you like a chunkier sauce.
In a large Dutch oven, heat the vegetable oil over medium-high heat, season the beef with salt and pepper, then sear it in batches until browned on all sides.
Remove the beef and lower the heat to medium, then add the onion, carrots, celery, and garlic, season with salt, and cook until the vegetables are softened.
Stir in the tomato paste and harissa paste, cook for 1 to 2 minutes until it darkens slightly, then add the crushed or blended tomatoes and stir everything together.
Add the pomegranate juice, ½ cup beef stock, and 1 tablespoon balsamic vinegar, bring to a boil, then reduce the heat to low and nestle the seared beef into the pot.
Tie the thyme and bay leaves with kitchen twine, drop them into the pot, cover, and transfer to the oven to braise for 3 to 3.5 hours until the meat is fork-tender.
Remove the beef from the pot, discard the bones and membranes, shred the meat finely with your hands or a spoon, then return it to the sauce and stir well.
Cook the pasta in heavily salted boiling water until al dente, drain while saving a cup of pasta water, then toss with half the ragu (or all if using 2 lbs of pasta).
Add pasta water a little at a time to loosen the sauce, stir in the Pecorino Romano and basil, then plate and top with more cheese, black pepper, and balsamic vinegar.