First off, have you already looked at the following page for places and timing?
https://www.japan-guide.com/e/e2011_where.htmlAlso if you haven't used it yet, familiarize yourself with www.hyperdia.com to find the best rail schedules, transfer info and fares. You'll easily find that if you want to go to the Tohoku area, you don't need to return to Tokyo - you can go via Saitama north of it.
As for what cherry blossoms are "better", it depends on your criteria. But you'll have a better experience if you see them in less crowded places like the Tohoku area unless you really want to see them in Tokyo and "enjoy" them like this:
https://imgur.com/V7xJXfaHonestly, I think you are overdoing it in some places. If you are already going to see the wisteria at the Ashikaga Flower Park, there is no need to take an excruciating day trip to also see them at the Fuji Kawachien in Kitakyushu. There are other places to enjoy the flowers since that appears to be your interest. The Showa Kinen Park near Tokyo is very nice. In Toyama, you might be able to catch the annual tulip festival.
http://fair.tulipfair.or.jp/en/Plus in Nagano is the Alps Azumi no Koen.
https://youtu.be/hLMCxLRLnowIn Mie, there is also the Nabana no Sato.
https://is.gd/czu2IbAnd you should not ignore the many gardens in Tokyo - some go back centuries. Your timing will be perfect to see the "secret" garden at the popular Sensoji Temple+Nakamise St that every first-timer in Tokyo rushes to. The garden is very tranquil and without the crowds, since almost nobody knows about it - it's only open a couple months a year.
https://youtu.be/b8Q5dcNWZqgThere are many others - Koishikawa Korakuen, Kiyosumi, Rikugien, Hama Rikyu, Kyu-Shiba Rikyu, etc.
https://goo.gl/tAECfMYou'll be delighted to find more as you head south as well - Himeji not only has the most famous original surviving castle, but the Kokoen Garden nearby is no less magnificent.
https://goo.gl/65ZtRiGet the combo ticket for both and one is virtually free.
Hiroshima City also has some jewels - it is
far, far more than just a city that got A-bombed. The Shukkeien Garden is one of the finest of the area, and if you want to see the hidden jewel of the city, go see the Mitakidera Temple - it's beauty and peacefulness is astonishing - and nearly completely unknown to the tourist guidebook "experts".
https://goo.gl/fAz4axIn addition to Miyajima being a very nice cherry blossom spot, don't skip Iwakuni as well just a bit farther south. Huge crowds will rush to Miyajima, but at Iwakuni you can actually see more blossoms than people.
https://goo.gl/NNQVrVSince the cherry blossoms come out later farther north, seeing them later in your trip makes more sense. You'll also be in the right season to see the azaleas, so don't skip those either.