ANA and JAL both have visit Japan airfares. You buy air travel coupons for anywhere within Japan which I think run USD 120 each (Y12,000 + 5% tax), minimum of 2. You can only buy these outside japan.

Otherwise, the japan rail pass is a good idea but you may want to limit yourself geographically. e.g., I was visiting a friend in N. Japan so only needed a rail pass on the JR East system. I got a flexible 4-day pass for Y20,000 (USD 200) which was good from NRT to Tokyo (worth $28 on the narita Express o/w and then worth $150 from Tokyo to Misawa). I think Japan Rail West has such a scheme. It will save you Y8,000 or so if you are only doing Tokyo and the Kansei Plain.