Relating to the post about delays, here is a paper co-authored by Tokyo Metro sujiya Mr. Kohei Ushida, who was profiled by NHK in their Professionals TV documentary. He is the inventor of the chromatic diagram, which gives a better idea of how delays develop in the running timetable. Though it doesn't cover the process of timetable recovery after accidents and bad weather etc, it does give you an idea of how timetables are managed and modified to make train run on time, or at least reduce delays.
http://www.railway-research.org/IMG/pdf/f1_tomii_norio.pdf