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Tokyo, Kyoto, and possibly Osaka.

SO. That's cool.

GET THE ******** JR RAIL PASS. SERIOUSLY.

http://www.japanrailpass.net/eng/en001.html

It will practically pay for itself if you're going to be taking the shinkansen between Tokyo, Kyoto and Osaka. Seriously. You can only get them from travel agencies before you depart for Japan. It's valid on all shinks except the Nozomi and Mizuho trains, which are usually special super expresses, i.e. the fastest trains. Other than Nozomi and Mizuho shinks, you can use it on ALL JR lines, local, express, super express, regular shinkasens. If you want to reserve seats on super expresses or shinkansens (including the fancy green cars) you'll have to pay extra for the reservations, but the regular fare will be covered by the pass.

If you need any trip advice, feel free to ask!