Tip
If you are only traveling between say Tokyo ,Osaka, Kyoto and Hiroshima consider a short duration National pass for the start and end of your trip to cover the long distances , then us local trains and purchase tickets (IC Cards) for the area you are staying in.
I found a good was to use a National Pass for a week to travel to the area I wanted to see ,
we stayed moved around that area for a couple of weeks and use the pass and pay for local trains. , the activate my next pass to the next fartherest point.
Or even consider taking a local flight or hiring a car to next destination
.