A few links of things I'd like to see in Tokyo if I had time (read: I'm not likely to, but I may be able to check one out at least).
Kobayashi Doll Museum - They don't seem to have a web page.
The Craft Gallery of the National Museum of Art. Japanese are good with their hands. One of my favorite pastimes is to sneak into depatos (department stores) and observe both the way food is displayed (in the basement floors) and how clerks handwrap packages (they pull out some magnificent designs. Japanese packaging is a league of its own). So, I can only imagine what a Japanse handcraft museum would include.
Tea ceremony. I'm sure this kind of things are tourist traps. But they got me at tea! Trap or not, nothing beats a good cup of matcha (powdered green tea).
This I'm really looking forward to. The National Theater of Japan has introductions to Kabuki, Noh theater and Bunraku (puppets!) Of course I'll doubt I'll see the three kinds this time but I'm tempted to.
Some extra tips: Cash is king in Japan. I know it's hard to believe, but you are MUCH better off with a bunch of cash than with your credit card. ATMs that take foreign cards are VERY hard to find, except at the airport.
Tax-free shopping. I've only used it for some expensive gifts, but savings can add up. In order for the shop to give you the extension, you MUST carry your passport with you, along with your address in Japan.
Cellphone. Most non-Japanese phones simply don't work in the country. The only place that I know where to rent a phone is at Narita airport. So, no matter how jetlagged you are, you'd better remember to pick up a phone (and remember also to return it when you leave!). The fee for a local phone (which can take but not make international calls) for 10 days was about 50 dollars (plus calls, including incoming ones).