Toss the beef in a large bowl with the cracked black pepper, 1 tablespoon thyme, the garlic, and the orange zest. Cover and refrigerate overnight.

Take the meat out of the refrigerator 45 minutes before cooking. After 15 minutes, season it on all sides with 1 tablespoon plus 2 teaspoons salt. Reserve the garlic and orange zest.

Preheat the oven to 325°F.

Heat a large Dutch oven over high heat for 3 minutes. Pour in 3 tablespoons olive oil and wait a minute or two, until the pan is very hot and almost smoking. Place the meat in the pan, being careful not to crowd it. (You will need to do this in batches.) Sear the meat until well browned on all sides. (This step is very important and should not be rushed; it will probably take 15 to 20 minutes.) As the batches of meat are browned, remove them to a baking sheet.

Turn the heat down to medium and add the onion, fennel, and carrot. Stir with a wooden spoon, scraping up all the crusty bits left in the pan. Add the thyme sprigs, bay leaf, and the reserved garlic and orange zest. Cook 6 to 8 minutes, until the vegetables are caramelized.

Add the crushed tomatoes and cook 2 minutes, stirring constantly to coat the vegetables. Add the balsamic vinegar and reduce to a glaze. Pour in the red wine and reduce it by half (about 5 minutes). Add the beef stock and bring to a boil.

Add the meat to the pot. Cover the pan with aluminum foil and a tight-fitting lid if you have one. Braise in the oven about 3 hours.

While the meat is in the oven, cut the whole tomatoes in half lengthwise. Pour 2 tablespoons olive oil into a baking dish in which the tomatoes will fit snugly. Place the tomatoes in the dish, cut side up, and season with ¼ teaspoon salt, pepper, and the remaining ½ teaspoon thyme. Roast the tomatoes in the same oven for 1½ hours, until they are shriveled and slightly caramelized on top.

To check the meat for doneness, carefully remove the lid and foil, being aware of the hot steam. Spoon a piece of meat out of the pan and press it with your thumb or a spoon. If it’s done, it will yield easily and almost fall apart. If it’s not super-tender, cover again and return the pot to the oven. When in doubt, taste it!

Take the pan out of the oven and uncover completely. Using a ladle, skim off the fat that rises to the top.

Turn the oven up to 400°F.

Bring a large pot of heavily salted water to a boil.

Ladle half the braising juices into a large sauté pan and add the olives. Return the meat to the oven for 15 minutes to caramelize.

When the water boils, cook the pasta to al dente and drain. Transfer the noodles to the pan with the braising juices and olives. Over medium-low heat, toss the noodles in the juices to coat well and bring to a low simmer. Stir in the butter, and season to taste with salt and pepper. Quickly add the spinach and a cup chopped parsley, and toss for just 1 minute, until the spinach begins to wilt.

Transfer the pasta to a large warm platter. Spoon the meat and its juices over the noodles. Tuck the roasted tomatoes in and around the noodles and meat. Sprinkle the remaining 2 tablespoons chopped parsley over the top.