I lived in Japan for a couple years (and I just got my place in Okinawa a couple weeks ago), I thought the train system wasn't too hard to navigate, but I can't remember the name of the big train hub in Tokyo. All the place names on the maps and signs are in roman characters as well as kanji, so you should be ok. Otherwise, just stand around looking confused at the signs and someone will come up and practice their English on you. Just give them your money and tell them where you're going and they'll work the ticket machine for you
. Sometimes they came up to help me when I wasn't confused, but they have the roman characters at a weird angle and I always had a hard time reading them. Maybe I always look confused...
You might want to look into taking a bullet train to somewhere else for the day and check Kyoto or Hiroshima out. I think that'd depend heavily on if you would have enough time to take the train, do something, and then take it back. So that might not be an option. I think Kyoto and Hiroshima are probably too far away for a day trip, but there might be something that isn't if you look.
I'd recommend climbing Mt. Fuji, but I don't remember what time of the year it's open for climbers. It gets kind of cold at the top, even during the summer. Depending on the weather, it could kind of suck. And don't get lost by going down the wrong side when you get to the top! It took me about eight hours to get to the top as well, so it's not an easy climb.
Akihabara has has lots of cool electronics/games/etc shops. There are also some sweet arcades, so if you want to get your *** kicked by Japanese kids, that's the place to be.
Roppongi is a shopping district, but it also has clubs/bars as well if that is your thing.
I may think of something else, it's been a few years. Pick up a survival language book and speak poorly in a Texan accent.
Aren't you in the .mil El? The New Sano hotel is pretty nice, or so I hear.