Hey,
Been living over here for about 6 months now loving it so far apart from the Japanese office!!
Food is really reasonable, you wont have a problem finding somewhere to eat at all..
Most menus have pictures so you can get away with smiling and pointing at things - ask for 'nama biru' if you want draught beer
Food wise, Okonomiyaki kinda like a omelet with noodles, seafood and other goodies and Yaki Niku - Korean barbecue are my favourites here!
Train tickets, you need to buy upfront. You could get yourself one of these;
http://www.japanrail.com/JR_japanrailpass.html
Failing that if you are in Tokyo and the surrounding prefectures then I would recommend getting a Pasmo or Suica card, its pretty much an Oyster pre-pay kind of thing.
It costs the same but its less hassle than going to a ticket machine all the time which you will probably do a lot in Tokyo.
Onsen - hot spring - well worth a visit, Shizuoka and Gunma have plenty and are fairly close to Tokyo. I found one through this site and it was amazing... http://www.secret-japan.com/onsen/
The one we ended up going too, http://www.amagisou.jp/
The lack of English can get a little frustrating on a day-to-day living basis, simple things like the post office and the supermarket is an adventure, but when I was on holidays here it wasn't such an issue at all...
If you can, I would try to visit Ishigaki Island, its in the Okinawa prefecture. There are tons of little islands around there with some really nice things to see. Much more relaxing than Tokyo!
Hope this helps, you will have an amazing time!
Cheers,
Ben