Things you may want to consider:
Two new Shinlkansen lines opened.
Takeo-Onsen to Nagasaki (Nagasaki shinkansen)
Kanazawa to Tsuruga (Hokuriku Shinkansen)
It will be Sakura season in Tohoku area. Expected days for full bloom are:
Hirosaki castle: 4/21
https://www.hirosakipark.jp/sakura/2024/03/14898/There are other type of late blooming Sakuras in the castle park.
It is hard to reserve room in Hirosaki in the Sakura season so you might have to get room in somewhat remote places. Even Aomori city there are not so many, and the room rate is high. One option is Asamushi onsen.
Kakunodate (Shidarezakura) 4/19
https://weathernews.jp/sakura/spot/3202/Senshu Koen, Akita city 4/16
https://weathernews.jp/sakura/spot/25/There are of course many other places of Sakura viewing.
In Kyoto it will be too late for Someiyoshino but other late blooming Sakura will be still in bloom.
Omuro-zakura in Ninna-ji: 4/11
https://weathernews.jp/sakura/spot/299/Haradani-en
http://www.haradanien.com/There are many types of late blooming Sakuras and other flower trees.
Take taxi from Kitaoji metro station.
Shinkansen travel is comfortable, but most of the route is not scenic. Several conventional (non-Shinkansen) lines have scenic places.
Kosei line Otsukyo-Makino (Thunderbird express): Lake Biwa. Take D seat.
Uetu line Murakami to Amarume (Inaho express): Sasagawanagare seashore. Take A seat.
Gono line from Akita to Goshogawara (Resort Shirakami): Seashore. Take A seat.
https://www.jreast.co.jp/multi/en/joyful/shirakami.htmlhttps://www.jreast.co.jp/railway/joyful/shirakami.html#routeHokuriku Shinkansen from Toyama to Takasaki: Northern Alps mountains, Asamayama. Take E seat.
At present Rikuu-Saisen line is closed due to road reconstruction which is very rare in Japan, so there are “substitute buses” which may be interesting experience.
If you use the JR pass extensively, you may better consider the Green pass, which is 30000 yen more expensive than the 80000 yen normal pass. Normally I use normal seat, but whenI went from Niigata to Akita with Inaho express, I took a green seat which is one of the spaciest seat in Japan.