Add onion and reserved neck and giblets and cook, turning until well browned, about 10 minutes. Add 4 cups water and bring to boil. When turkey is done, transfer it to a platter and cover loosely with foil. Remove extra stuffing from oven. Pour pan juices into a wide bowl and use a ladle to skim off fat.
Place roasting pan over high heat and when it starts to sizzle, stir in the turkey stock.
Reduce heat to moderate, stir in reserved pan juices and simmer 5 minutes. In a small bowl, mash the remaining 2 tablespoons butter with the flour. Whisk this paste into gravy, bring to boil and whisk until smooth. Reduce heat to low and keep warm, stirring occasionally, while you carve the turkey. Season to taste with salt and pepper.