You don't need the rice ;-) It just fills you up, and trust me, you don't want to be filled up on inconsequentials
"Sushi," btw, just means the rice (with or without the extra stuff); Sashimi is the raw fish. This fish is so incredibly fresh and flavorful, you'll never be able to eat sashimi elsewhere again (well, you will, but the comparison will always be in your mind, and you'll never be able to eat inferior stuff
). Oh, and make sure you just let the chef choose for you. If there's something you absolutely do not want to eat/try, or something you really really want, let them know; they know what's best, freshest, and most flavorful that day, and the good ones can gauge how much you will eat without even asking (the term is "omakase" = I will entrust it to you). Even if you don't want to eat it, go to the market, it's really neat to visit. Just don't get run over by the crazy cart drivers.
My mother, who is extremely picky about accommodations, said that she would stay at K's house again, if that's any indication. It's not all that expensive either. If you're going with a group, you can probably get one of the "dorm" type rooms for yourself. IIRC, most Japanese hotels and the like charge per person, rather than per room. We spent most of our time in Kyoto; I don't remember the Tokyo one well, but it was decent. It's a nice clean facility, newish, has a decent kitchen, very close to the main Kyoto train station (like, 10 minute walk), has a western-style and a Japanese-style table to sit at for eating, a lounge area, and a saltwater fishtank for entertainment
You will, btw, be shocked at the prices for produce, especially, out of the groceries if you're going to do any cooking yourself.
If you're at all interested in anime, the Ghibli museum is in Tokyo and was pretty fun. Try to avoid the last day they're open for the season, especially if it's raining (not that I have any personal experience with this or anything...
and not that I have a problem with little kids running around everywhere...). The other drawback would be that almost all of the more interesting signs were in Japanese, but even just looking at the displays was neat (I went with my mom, who is the Japanese part of my family, so she read the signs to me
But that was after I went through once, then found her and got her to read the more interesting-looking signs)
See if you can get in to visit the Imperial palace and gardens - I seem to recall that you have to sign up for it somehow, but most tourbooks probably have information on that. There are a TON of temples in Kyoto that are totally worth it as well; they have one or two of their major bus lines set up specifically for tourists who want to See the Sights. I'm sure any of your basic tour books has information on all that stuff. We went out to Byodo-in, which was kind of cool. Of course, you have to stop by Kinkakuji.
I did a day trip (I forget if it was from Kyoto or Tokyo) to Hiroshima and nearby Miyajima. The Hiroshima part was amazing in a lot of ways (good and bad). We spent a half day at each, which was enough time (longer might've been nice, but it was adequate, and I'm one of those that tends to read almost every sign when in a museum). You need to have a Hiroshima-yaki (okonomiyaki + fried noodles (and I think an egg?), while there. Of course, you should go into an okonomiyaki shop in general - there was a good one at the top of the Kyoto train station).
You can get a Japan Rail pass of some form (I think it was mostly for JR trains - there's two main train systems) that is discounted and you can only get if you're a foreigner (If you ever get a hold of your friend in Japan, the "native guide" is allowed to get one as well, but there's a limit on how many native guides you're allowed). I think the one we got was good for a certain number of days, so we used those days to take the shinkansen to go on longer trips (I believe that involved the Kyoto-Tokyo, and back, up to Fuji-san (we spent a night there) as well as the trip out to Hiroshima).
There are also some more remote temples and things that are worth getting out to if you have the time. Fushimi Inari has the fox spirits all over the place as well as the lines and lines and lines of torii - interesting to see. If you can afford it, try to spend a night at a nice ryokan (Japanese style inn) with a good furo. Depending on the ryokan and the size of your party, food is served in a big room for all the guests at the same time, at long tables on the floor, or in a Western-style room, or in your individual room. They tend to very traditional Japanese type meals (includes grilled whole fish and miso for breakfast!). These places will have communal furo (baths) - one for men and one for women - typically have at least part of it outdoors. There will be a big area where you sit on a little stool and wash yourself with a hand-held shower head, then you go soak in the big hot pool of water. Mmmmm...
Japan is more and more Western Tourist friendly. More and more signs are in English (or Engrish) and/or have romaji (English letters sounding out the Japanese) to help you get around. The average Japanese person's English skills are questionable at best, but you can probably get around without much/any Japanese.
Visit a Mr Donut and get a Pon de Ring (I think? they look like donuts made up of a ring of donut holes) which are surprisingly good. McD's often has Rather Interesting Selections (at least to Americans... they're normal to the Japanese... when I was there, they had Marron Pies (chestnut cream pastries) that were really really good...).
The Japanese Tourism website at least used to be a decent resource. I will let this thread percolate in my head another day or two, more things might surface