Hi Joanne - I find the best way to research train schedules is to use Google Maps. Play around with the times if you're planning to use a shinkansen and local train, as in a city like Tokyo - various options may appear with a simple change of the time.

Also note some train & bus schedules like country local ones may not be updated till a month in advance depending on the season - you can again get a rough idea from google maps, from earlier dates.

With local country trains & buses - playing around with departure/arrival times on Google Maps will help too.

If you wish to book train tickets online  (generally only available a month in advance & depending on which train lines) - use EKI NET (english website)
https://www.eki-net.com/en/jreast-train-reservation/Top/Index

this only covers JR East areas - hope that helps

I agree that Google Maps is a great starting point. I used it on my last trip to compare routes, and it was surprisingly accurate for finding the quickest connections between cities.

Another tip is not to stress too much about booking everything far in advance unless you're traveling during a major holiday or peak season. The shinkansen runs very frequently on popular routes, so there's usually a good amount of flexibility.

For your itinerary, Tokyo to Nagano is straightforward on the Hokuriku Shinkansen, and then Nagano to Kyoto usually involves one transfer, often at Tsuruga or another major station depending on the service and timetable.

Have a fantastic trip! Japan's train system can seem a little overwhelming at first, but once you've taken your first journey, it becomes much easier to navigate.