Which routes are included?

Hi, I am travelling to Japan in May 2024. I want to go to Hokkaido first, then pass through Aomori, Hirosaki, Akita. Then further to Tokyo and other big cities such as Kyoto, Osaka etc, and further probably to Hiroshima. We do have three weeks, so we do have quite a lot of time. However, I was wondering if the routes that are not covered by Shinkansen (e.g. Aomori to Hirosaki) are included? Is every train operated by JR included? If not, which ones are and which ones are not?

Thank you so much!

Astrid