Lived there (Tokyo) for six years, generally speaking Tokyo is very english friendly. You should be able to find a Metro Tokyo train/subway map in english. If you are a Palm user there is a palm application called MetrO that will route you on the train/subway with shortest route/fewest transfers etc... PM for details if you cannot find it via google, I think it is freeware stuff, pretty good. You just need to download the database for Tokyo area and install it.

Get a good pocket size English-Japanese dictionary, most good bookstores will have one. It will be worth the $10-15 if you are out on your own and need help. Have your hotel print a "help card" for you to hand a taxi driver, includes kanji directions back to where you need to go, could save your bacon.

Mt Fuji is only climbable (sp) in Aug/Sept, one of the best experiences is climb all night, be there for sunrise, check the wx, don't go if it is cloudy/crappy. Bus will take you to about 4000' then you climb up from there, remember to come down the same trail you go up elst you have a new challenge getting back to your lodging Old Japanese proverb says a wise man climbs Fuji once, a fool climbs it twice......

Bullet train is a great experience Check with your travel agent, as recent as a couple years ago, one could buy a tourist train pass that was good for unlimited JR train usages for a period of time, including the Shinkansen! Worth every penny if you plan on using the Shinkansen. You will still need to pay seperatly (sp) for non-JR line tickets in the Tokyo area. See your travel agent for details. PM me if you cannot find it.

Kyoto is often best done as part of an organized tour, fascinating place.

Good luck, enjoy the trip