Great decision! I spent 3 weeks in Japan and absolutely loved it. Your right though, 2 weeks won't even scratch the surface of Tokyo.
Most of what I would say has been said already but I will add a few notes.
Embrace the train system in Tokyo (or in any city for that matter). It's cheap and it will get you anywhere you need to go.
Be prepared for the heat. No one thinks of Japan as hot but I went in August and it was the hottest weather I have ever experienced. Every day was around 37 degree and 95% humidity. However, I'm not sure what it's like in June.
I have been to many countries and I believe Japanese people are the kindest. I say this because just when you think your completely lost (a definite in Tokyo) a perfect english speaking person will come to you and offer their assistance. I witnessed this in every city I went to.
Every major city has it's trademark food. I wish I could tell you them but I am not even going to attempt to spell them out. I highly recommend Hiroshima's dish and Osaka's.
Just like the food, every city and town has it's own shochu... not sake... shochu. I personally think shochu is much better, plus it's cheap and strong.
Expereience the high speed trains... unexplainable. Try to avoid the smoking cabins though.
Expereince Kareoke prefferably with Japanese people. It doesn't matter how bad of a singer you are they will make you feel like a rock star.
Just as Ozy_Flame said, the Japanese women love white guys and they are very forward about it. I was on the trip with my wife but that didn't stop them from eye screwing the hell out of me.
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