I, too, love Japan.
If you go, you must try staying at least once at a traditional Japanese hotel--a ryokan.
This site is excellent--it's a free service, which takes away language problems for you! They even give you a print out with names and directions in Japanese so you can show it to a taxi driver (cleanest taxis in the universe in japan, by the way).
They have detailed instructions on the cultural expectations so you feel you know what you are doing.
http://www.japaneseguesthouses.com/index.htm
We used it to stay in monastery on Mt. Koyasan! It was a fantastic experience. We stayed at this one:
http://www.japaneseguesthouses.com/d...hojoshinin.htm
The trains are clean, efficient and totally safe--use them!
Favorite places (all very safe): Kyoto, Mt. Koyasan, Takayama (a bit of a train trip but a mountain town where Japanese tourists go)