Preheat oven to 375 degrees.
Sprinkle salt and pepper over the short ribs and dip them in the flour on all sides, dusting off the excess.
In a large dutch oven, slowly sauté the bacon over low heat, allowing the fat to render without burning the lean part. Cook until bacon begins to brown but is not fully cooked or crisp yet.
Meanwhile, in a separate sauté pan, heat the olive oil and sauté the short ribs to brown thoroughly on all sides. Remove from heat and set aside.
In the pot with the bacon, ad the onions and cook until the onions start to caramelize, about 10 minutes. Add the garlic and cook until fragrant, about 1 minute. Add the red wine, carrots and celery, scraping up the bottom of the pan to deglaze. Simmer until the wine has reduced by half.
Add the tomatoes the pot. Add the thyme bundle and the short ribs back to the pot and nestle them in bone side up. Add enough beef stock to almost cover the ribs. Cover and bring the mixture to a simmer, then remove from the heat and place in the pre-heated oven. Cook, covered, for approximately 2 1/2 hours until the meat is fall of the bone tender.
About 15 minutes before the short ribs are done, cook the pappardelle according to package directions, until al dente. Drain the pasta reserving about 1 cup of the pasta water.
Remove short ribs from the oven. Remove the short ribs from the pot and carefully remove the bone and any cartilage. If there is a lot of fat in the pot, strain some of it off the top using a large spoon. Discard the thyme bundle. Shred the meat with two forks and return it to the sauce. Season the sauce with salt and pepper to taste. If the sauce seems too thick, stir in some of the pasta water to thin it out.
Toss the desired amount of pasta with the sauce and serve topped with grated parmesan.
Enjoy!