The best Sakura hunting is a matching of the best Sakura site and the best weather day. You have already chosen good base sites with many attractions; Tokyo, Kyoto, and Osaka. Also, you have allocated reasonably long nights for each. It should be enough to wait for a good weather day to visit a Sakura site. You now have a nationwide train pass to visit any Sakura site in Japan, too. So, you just have to prepare some sets of Sakura sites to find the best match with Sakura and weather status.
Here, I compared a list of the 100 selected cherry blossom sites in Japan with Sakura forecast data by a weather company WeatherNews.
https://ja.wikipedia.org/wiki/“ú–{‚³‚‚ç–¼Š100‘I
http://weathernews.jp/sakura/The following lists full bloom date forecasted by WeatherNews, Sakura destination name, the nearest JR station, and the weather forecast link, which also includes the official link and a link to "MAP".
Apr 10 Fukushima/Miharu Takizakura (JR Miharu, 20 min bus)
https://weathernews.jp/s/sakura/spot/71/index.htmlApr 10 Nagano/Garyu Koen (JR Nagano, Nagaden train to Susaka, 20 min walk)
https://weathernews.jp/s/sakura/spot/4803/index.htmlApr 10 Nagano/Takato (JR Inashi, 25 min bus, 15 min walk)
https://weathernews.jp/s/sakura/spot/165/index.htmlApr 11 Nagano/Kaikoen (JR Komoro, 3 min walk)
https://weathernews.jp/s/sakura/spot/162/index.htmlApr 12 Niigata/Ogozu Bunsui (JR Bunsui, 20 min walk)
https://weathernews.jp/s/sakura/spot/227/index.htmlApr 12 Niigata/Muramatsu Koen (JR Gosen, 15 min taxi)
https://weathernews.jp/s/sakura/spot/226/index.htmlApr 12 Osaka/Zoheikyoku (JR Osaka-Tenmangu, 15 min walk)
https://weathernews.jp/s/sakura/spot/318/index.htmlApr 15 Yamagata/Eboshiyama (JR Akayu, 20 min walk)
https://weathernews.jp/s/sakura/spot/63/index.htmlApr 16 Fukushima/Tsurugajo (JR Aizu-Wakamatsu, 5 min bus)
https://weathernews.jp/s/sakura/spot/70/index.htmlApr 16 Ibaragi/Shizumine Furusato Koen (JR Shizu, 30 min walk)
https://weathernews.jp/s/sakura/spot/4001/index.htmlApr 21 Akita/Senshu Koen (JR Akita, 10 min walk)
https://weathernews.jp/s/sakura/spot/25/index.htmlApr 22 Iwate/Takamatsu no Ike (JR Morioka, 20 min bus)
https://weathernews.jp/s/sakura/spot/40/index.htmlApr 23 Iwate/Kitakami Tenshochi (JR Kitakami, 15 min bus)
https://weathernews.jp/s/sakura/spot/34/index.htmlYou may pick some, or drop some of them. Then, keep watching the remaining until the very day to hunt Sakura there. Both Sakura and weather forecasts should be updated. Just pick up the best weather day for some of them, and go there with your pass.