Beware that the Japan Rail Pass can't be used on the Nozomi shinkansen (bullet train). I was travelling Fukuoka to Tokyo and back via Kyoto and Hiroshima, and this limitation would have put a severe kink in my travel plans if I hadn't spotted the small print in time.
Sure you can plan round it if necessary though. I've used the Swiss Rail Pass which is the same idea, and it certainly did pay for itself in just one day of (admittedly long and tortuous) cross-country rail travel.