Sakura forecasts:
https://n-kishou.com/corp/news-contents/sakura/news2017.htmlhttp://sakura.weathermap.jp/
If there are still sakura in Yoshino on the 14th then good. If the pattern this year is on average (although none yet published for Yoshino) or the same as 2016, 4.12 is considered already as the end of season there:
http://www.japan-guide.com/blog/sakura16/160412_yoshino.htmlElse, you would want to see sakura in last hurrah in Hokkaido on last week of April until first week of May but you do not want that. More info here in Cherry Blossoms Report 2016 here in Japan Guide.
You're itinerary is good yet you are moving way too much of your luggage from one place to another. Well, it is your choice. Mind you that the travel alone takes a lot of time, especially Yoshino-Miyajima and Miyajima-Kanazawa among others.
If I have to do your travel, I will consider first Koyasan then tour to Yoshino or forego one of them before settling in Osaka. I will have Osaka as my base as I can move freely from there to Kyoto, Nara and Hiroshima/Miyajima and Himeji as day tour prior going to Kanazawa.
From Kanazawa, bus is the best way to get to Shirakawago and to Takayama then take the bus from Takayama to Matsumoto/Kamikochi or even Fujisan but there is Alpine Route along the way. So instead of moving to Kanazawa, I will have to move first from Osaka to Takayama (train or bus), then bus to Shirakawago and eventually to Kanazawa.
If ever I stay in Shirakawago after Takayama, my next base will be in Toyama as the travel from Kanazawa to Toyama or vice versa is already a breeze via shinkansen and for early start option of Alpine Route in the following day/s. Since I only wanted to move as little as possible, I will only have day tour in Shirakawago after Takayama, arrive in Kanazawa by bus and travel from there to Toyama. Buses from (if ever, Osaka to) Takayama to Shirakawago to Kanazawa is not included in JR Pass.
As I start Alpine Route from Toyama, I will end up in Nagano or Matsumoto after. I will have the base of Matsumoto to travel to Kamikochi then go down to Nakatsugawa for Magome-Tsumago trail the next day before getting down to Nagoya or eventually to Odawara or Tokyo for Fuji/Hakone Tour.