I would go to Daikoku Futo PA(parking area) on the wangan in tokyo on a friday night or saturday night to see all the crazy street racers if you like that scene. They also have vans with giant subs and speaker blasting techno, its pretty chill.

As for sights I went to Mt Fuji and it was beautiful, try to go there on a clear day. Hot Springs in Hakone near Fuji are very relaxing and it would be a good idea to stay at a old style hotel there. Tokyo is great for shopping and the nightlife. Kyoto is beautiful and you should go to Neji(sp forgot the exact name but i think it was Neji or Neiji) Castle and the Geisha streets. Hiroshima has a very interesting museum about the atomic bomb right where it struck. Overall japan has a HUGE list of things to see and do.

Main tips
Trains are an amazing and cheap form of transportation in ALL of Japan.

100 yen = 1 dollar pretty much and prices are similar to American prices

Try to stay at authentic places, (like places with Tatami mats and sliding doors, the stereotypical stuff) I did and I enjoyed staying at places like that too.

Go out of Tokyo, the nature in Japan is some of the most beautiful in the world.

best views/sights in Japan can be seen and experienced in the mountains. Mt Fuji is the most popular but does not rank highly in best views in my opinion.

also, you can get a great view (and free) from Municipal Bldg in Shinjuku. Interesting buildings that look like they were assembled with legos.