paulovey
The first suggestion would be to Google search this group; lots of good advice has been given in the past and you can get loads of ideas.
The basics:
You'll almost certainly need a rail pbutt; they're a great deal and it will pay for itself many times over. You should be able to get one from by clicking the English link you get to a great site to help plan rail travel.
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The key areas folks visit are Tokyo and Kyoto, with various other destinations added for a longer trip such as yours. I suggest not moving around any more than you have to; find a good place to stay in Tokyo and base regional travel out of there (Kamakura and Nikko are some examples of side trips from Tokyo). Do the same with the Kansai region (the area around Kyoto-Osaka). My personal suggestion for the latter would be to stay in Osaka. For one thing it's more central to the other places in the region you'll want to visit (Nara, Mt. Koya, Himeji, even Hiroshima for a long day trip); for another it has more night life, but a lot depends on exactly what you define as night life.
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I can't help when it comes to beaches. Those around Osaka where I've spent most of my time are not worth visiting. I've visited some up on the Japan sea side, but they're not great beaches. However, I do suggest you travel in that area. If you don't carry much luggage you could break up the trip from Tokyo to Osaka-Kyoto by a day or two traveling that less-developed coast. I really like that part of Japan. It's actually a very beautiful place to drive if you're up for the challenge. In the rural areas you'll find more temples-shrines and other spots that are not easily accessible by train.
For travel preparation I suggest going to the library or book store and reading through several guide books to see which one you like. Most information you need is on the Web; each prefecture will have an English Website that contains local information, but you might not always have Web access when traveling, if at all.
Hope this helps!
John W.