Here is another thought to consider. You might try to find your answers from someone in the dairy industry, where most of the product (milk) is moved around the plant in pipes. They have to meet very strict sanitary conditions and must clean the piping systems after each shift or batch because of the fast growing bacteria in milk and cheese processing. The dairy industry uses some pretty strong cleaning solutions in their piping systems, most of the pipe is stainless steel and either welded or gasketed joints. It is all above ground, but I should think they may have solved most of the problems you face.