Referenced above, the HyperDia website is helpful in planning rail travel. HyperDia | Timetable and Route Search in Japan.

For HyperDia, IF you will be using a JR Rail Pass, then be sure to go into "More Options" and untick the box for "Nozomi/Mizuho/Hyabusa (shinkansen)" as those trains are not eligible with the JR Rail Pass. As Jib71 noted, the Rail Pass would not be worth the cost unless you will be including the round-trip Kyoto-Tokyo-Kyoto in your itinerary. Otherwise, just make rail reservations and buy tickets at the larger JR Station such as Kyoto and ride the Nozomi.