1. Preheat the oven to 425ºF and line a roasting tin with foil.
2. First prepare the pulled pork. Combine the sea salt, sugar, paprika, cumin, garlic granules and cinnamon in a bowl. Mix well to combine.
3. Pat the pork shoulder dry using kitchen paper and remove any string tying it together.
4. Cover the pork shoulder in the rub, making sure every part is well covered. Put in the lined roasting tin and cook at 425ºF for 30 minutes to seal.
5. While the pork is cooking, make the basting juice by combining the apple cider vinegar, ketchup, cayenne, brown sugar and paprika. Set half of this aside, use the other half to baste the pork during the cooking process every hour.
6. After 30 minutes remove the pork from the oven and baste with the mixture, decrease the oven temperature to 285ºF and cook for another 8 hours, basting every hour.
7. Once the pork is cooked remove from the oven and pull using 2 forks. Place in a clean roasting tray, combine with the remaining basting juice, ensuring the base of the roasting pan is evenly and completely covered and set aside.
8. Increase the oven temperature to 425ºF.
9. To make the macaroni bring a large pot of well seasoned water to the boil, add the macaroni and cook for 6-8 minutes, till al dente. Reserve a cup of the starchy pasta water and then drain the reminder of the pasta through a colander. Run over cold water to stop the pasta cooking.
10. Make the cheese sauce by melting the butter in a medium saucepan over a medium, low heat, once melted add the flour, stir well to combine and keep stirring the roux for several minutes to cook through all the flour. Add a small amount of milk and stir through, the roux will thicken up, add a little more and repeat. Gradually the paste will start to look more like a sauce, keep adding the milk and once it is resembling a sauce add in the thyme and bay leaves. Once all the milk is added, add the cheeses, tomatoes, chilli flakes and salt.
11. Cook for a further 5 minutes, remove the bay leaves and then stir through the cooked macaroni. Place the macaroni mixture on top of the pulled pork. Scatter the breadcrumbs and cheeses over the top and cook for 20-30 minutes. Serve immediately.