Once all the milk is added, add the cheeses, tomatoes, chilli flakes and salt. 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. Add a small amount of milk and stir through, the roux will thicken up, add a little more and repeat. 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.Run over cold water to stop the pasta cooking. Reserve a cup of the starchy pasta water and then drain the reminder of the pasta through a colander. 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.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. Once the pork is cooked remove from the oven, and pull using 2 forks.After 30 minutes remove the pork from the oven and baste with the mixture, decrease the oven temperature to 140 and cook for another 8 hours, basting every hour.Set half of this aside, use the other half to baste the pork during the cooking process every hour. While the pork is cooking, make the basting juice by combining the apple cider vinegar, ketchup, cayenne, muscovado and paprika.Put in the lined roasting tin and cook at 220C for 30 minutes to seal. Cover the pork shoulder in the rub, making sure every part is well covered.Pat the pork shoulder dry using kitchen paper and remove any string tying it together.Combine the sea salt, sugar, paprika, cumin, garlic granules and cinnamon in a bowl. Preheat the oven to 220C fan and line a roasting tin with foil.