Start by refrigerating the meat grinder equipment if possible. Do not trim the fat. Cut the pork shoulder into small 1/2 inch pieces. Chill the pork until very cold, freezing it partially if possible.
Fit the grinder with a medium grind plate. Once the meat is cold, grind according to manufacturing instructions. Return the ground meat to the fridge to keep cold. Clean and sanitize the grinder equipment and return to the fridge.
Use a blender or spice grinder to coarsely grind the fennel seeds. Add the fennel seeds to a bowl along with the pepper and chili flakes. Weigh out the kosher salt and add to the spices.
To make the sausage filling, add the ice-cold water to the ground pork along with all of the spices. Use your hands to mix the water and spices into the ground pork. Spend a few minutes kneading the pork mixture until it becomes sticky. Chill the mixture while preparing the sausage stuffer.
Soak the natural pork casings in warm water for an hour. After soaking, flush water through each of the casings. Stretch the casing around the faucet and run warm water to inflate the casing.
Assemble the sausage stuffer according to package instructions. Lightly grease the stuffing horn. Take a single casing and begin to slide it onto the stuffing horn, scrunching it up so that the whole casing is threaded onto the horn.
Slide a few inches of casing off the tube before beginning to stuff the casings. Use your hand to slowly guide the sausage out of the horn in one long coil. Try to keep the sausage even in thickness while stuffing and do not overstuff the casings or they might burst while cooking.
Continue to stuff the sausages until you run out of casing. Be sure to leave a few inches of casing at the end. Repeat with new casings until all the meat is used.
Use a pin to evenly poke holes in the sausage and remove any air bubbles. Tie off the casings at both ends of the coil. Pinch the coil where you want to make a link and twist the sausage several times to create the link.
To ensure the links don't unravel I like to tie a piece of twine between each link. The twine can be removed after cooking. The sausages are now ready to be cooked and can be frozen if desired.
