Train timetable

HI

End of October I planing three-week trip to Japan.

Approximate plan is as follows:
Tokyo 1-2 days
Train to Sapporo. Sapporo 2-3 days and the around
Sapporo-Nagano 3-4 days Japosnke alps. (Takayama, Shirakawe-go...)
Kyoto 4-5 days. Kyoto around
Himeji- Hiroshima and Miyajima
Can anyone recommend some place or, playground, which is worth a visit? I'm also a big fan of photography and I am interesting for photo corners. I also love trekking. I will be very glad to any advice, something was still worthwhile
What you may be seeing in Saporu and surrounding areas by public transport?

On page Hyperdia I'm a little check train timetables. Here I am a little confused, because I do not know which trains can use with JR Pass.
I checked the train route from Tokyo to Sapporo. For JR pass there si not any fest train. all trains spend all day:
Tokyo 9.08 Sapporo 21:57...
14.20- 6.07 Sapporo.
I hope, I watch right or timetables for my train.... also, there so night trains. How is sleeping on Japan trains? There is enough space for someone who has longer legs?

Thank you all for the help and advice

Zee