Reservations, main station in Tokyo & finding full schedule of trains

Hi there!

Here are some answers for you:

1. For reservations you will unforutonatley need to be in Japan at a JR ticket office with your JR Pass. But don't worry, most trains also have non-reserved seating, and there are generally many seats available on all trains provided you are not planning on travelling during rush hour.
2. You can learn how to use Hyperdia for JR Pass holders through our video blog. We describe how to only select JR trains here.
3. There are many JR stations in Tokyo, however there are only 2 bullet train stations which you will use for long-distance travel: Tokyo and Shinagawa station. For Kyoto and Narita you will probably be best using the main Tokyo station: "TOKYO" in hyperdia.
4. The last train from Takayama to Kyoto leaves Takayama at 18:45, arriving into Kyoto at 21:58 (193 mins). You can select "Type: arrival" in the hyperdia options to look for trains that arrive around a certain time rather than depart.
5. For the all the trains for a specific day to a specific place you should click the "station timetable" link in the search results from Hyperdia. Please see the image below for the location of the link in the hyperdia search results:

Hope this helps!