Kinda late, but have fun man. Japan's a wonderful country, I'm sure you'll love it as much as I do. So you plan on going all over? Lucky. I've always wanted to tour around Japan, but it would cost an arm and a leg. I've been to Tokyo, Yokohama, Sendai, the Aichi prefecture (Nagoya, Kyoto, Takayama), so if you have any questions about those places, then let me know! You can seriously blow off a good 3 weeks in Tokyo alone...because it's so freakin' huge. In fact, I think I blew off 2 weeks in Akiba alone last summer. XD There's so much to see over there!
My favorite places in Tokyo:
Akihabara- Every otaku's dream
Harajuku- If you're into J-pop, they have a ton of idol shops here...including the Hello! Project store. They also have the Yoyogi arena just around the corner, and lots of artists hold concerts here during the summer. You'll see lots of goth loli's here! If you have time, get a crepe from one of the stands. Some of the best crepe you'll ever have!
Shibuya- Definitely the fashion district, where you'll see a lot of fashionable people.
Shinjuku- Some nice shops here and there, and the red light district! (kabuki-cho) if you're into that kinda thing, haha.
Suidobashi- Right next to the Tokyo Dome. I think anyone should go to the Tokyo Dome at least once. It's amazing at night.