Oh Sushee I am so excited for you and so jealous. I have been twice - the first time I lived there for a year as an exchange student and the second time was 13 years later and boy had things changed. I love the place so much. I could write an essay for you on all the things to do, especially if you love getting off the beaten track and into the cuture. Lucky for you I don't have time to do it now. But if you are interested let me know and I'll post more details. Off the top of my head, I would recommend Tokyo (just to say you've been there, I wouldn't spend too long there), Kyoto, Sapporo, Hiroshima and maybe Nagoya and surrounds (I lived in a beautiful country town near-ish to Nagoya and the attractions in the general area include hot springs and cormorant fishing).

You are going to have such a great time. You lucky thing.