Getting Around
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I gave serious consideration to renting a car in Japan but ultimately followed the good advice of many travelers to rely on the excellent train system in Japan.  As it turns out, taking the train is itself a lot of fun in Japan, they are run so efficiently and with such great service.  We bought 14 day rail passes which were a joy to use, allowing us unlimited use of the train for two weeks, including all but the fastest bullet trains.  I chose to buy second class rail passes and did not regret it - many trains did not seem to have first class cars anyway and we I could not see any advantage to traveling first class,  especially since we could get free reservations in second class with our rail passes anyway. 

Getting (free) advance reservations when we did was very useful, not simply for the peace of mind in knowing that we had a seat on the train.  Each reservation ticket itself showed the name of the destination (and origination) in Kanji (and in English for the larger stops) as well as the departure and arrival time, and the number of the train itself.   We made most our reservations in Kyoto with the help of an English-speaking volunteer guide who left her post across the hall from the reservation desk to assist us.  Some of the connections we made getting from Kyoto to Matsue to Hagi to Hiroshima to Shizuoka were rather complicated.  Having reservations, and tickets to tell us exactly when we were going was great.