I had a trip to Japan in this past October. I had lots of train troubles in this trip. The train operation is usually very stable and reliable in Japan. But a train suspension and/or a train delay may happen on your trip.
I will explain how to deal with these problems, with my experience.
***I updated this following information on November 5, 2011.***
Between Shirahama (白浜) and Kumanoshi (熊野市) on Kii line (紀伊本線) in Kii peninsula were closed due to huge typhoon. JR West and JR Central announced they will complete to restore on December 3, 2011. Continue reading Operation status on Kii line