Here's a tip for Tokyo dining on the cheap (besides the many Ramen shops): Go out and buy a little containers of toothpicks and go to the food displays at Mitsukoshi or Daimaru department stores. The amount of free food samples there is astounding!
Tokyo is definitely a walking city, and its train system is second to none—there's practically no such thing as a late train in this city. If you're planning to travel to other parts of Japan, definitely consider picking up a Japan Rail Pass. The pass, which is sold in 7-, 14- and 21-day increments, is valid on most trains, including the speedy bullet trains, buses and ferries (there are some restrictions). Then I suggest getting out of Tokyo and into Kyoto, and, if there's time, to Kobe and to the memorial at Nagasaki.
Get out of the tourist traps with Peter's off-the-beaten-path guide to Tokyo.