Hopefully you made it to your destination well rested.
You could spend a lot of time in Tokyo and still not see everything. It is not all Japan of course, so be sure to also get out and see the country.
In Tokyo a few of the best places to see are the Tsukiji Fish Market, plus the site that every last tourist goes to see, the Sensoji Temple. If you are in Tokyo on a Sunday afternoon, be sure to go visit Harajuku to see the youth with their wild fashions. Meiji Shrine and Yoyogi Park are next to it and well worth seeing also. And be sure not to miss the Shibuya Hachiko intersection especially on a weekend when it looks like half the city is crossing the street all at once.
Take a few good day trips to Nikko, Kamakura/Enoshima, Hakone or the Fuji 5 Lakes Area.
There are gegional passes from Odakyu to see Hakone and the Fuji area.
If you can, try to find a little time to see the Japanese themselves. Go visit a Japanese supermarket and see what people typically eat. Look through a park and watch the Japanese kids play. Learn about the history of some of the places you visit before your departure - it will give your trip so much more meaning.