An excellent resource for those looking for Veg*n fare in Tokyo is Hiroko Kato's http://www.vegietokyo.com. She also has several articles in the info for vegetarians section on how to eat Vegan in a Japanese Restaurant.
Handicap accessibility in Tokyo is much improved. Reforms in the past few years have made access to restaurants much easier. This is not the case in more rural areas, so please be cautious. Regardless, almost all buildings have ramps and elevators.
Japan has a love affair with tobacco. Most (99%) restaurants allow smoking. Though some will have a non-smoking section, odds are sensitive people will still be affected. This is currently changing. Effective March 2007, many public spaces, such as shinkansen, will be mandated smoke free zones.
Vegetarians and Vegans alike must be extremely careful in Japan. The presence of katsuo (derived from the fish bonito) is omnipresent. Even noodles are boiled in this broth, in lieu of water. Many shojin ryori places outside of Kyoto do not adhere strictly to the philosophy of temple cuisine, and serve fish dishes. Places of higher repute are extremely accommodating, but you should try to allow them warning.
Bakeries are excellent options for vegetarians in Tokyo, thanks to several high quality local chains. Take your time to ensure that there is no sausage, seafood, and bacon (a favorite here) in seemingly innocent looking rolls. Many breads are washed in egg, so steamed breads may be the only option for Vegans.
Vegans have free reign at higher quality traditional sweets stores, such as Toraya, which uses arrowroot for their thickening agent in adzuki jellies.