In continuation as there is too much to unpack in a PM (am also uncomfortable for my suggestions to not be scrutinised as I am very capable of making errors).
What you need to do now is get a guide book/decide on travel sites and plan. The problem with visiting cities in Japan is that the architectural vocabulary is completely different to what you might already be familiar with (you haven’t said where you’re from), without knowing how to read Japanese there won’t be enough clues to tell you what you are looking at, so unless you are expecting to find something you very likely wouldn’t know it was there. It’s very easy to walk past museums and restaurants thinking they are ordinary houses or offices.
I’d suggest creating your own personal map (“my map” in Google is perfect for this) and start pinning a wish list which will help you theme your visit and prevent you criss crossing cities unnecessarily. You will also be able to discover attractions on the map that you might not have known were there - even by being there in person.
Depending on where you stay, the combined Toei Subway and Tokyo Metro ticket might be the cheapest way to explore Tokyo, particularly if you can use the 72hour version. Otherwise, just use precharged PASMO or SUICA card (these can be used in Osaka and Kyoto too)
info on the subway/metro pass -
https://www.tokyometro.jp/en/ticket/travel/index.html this can potentially limit your travel spending to 500yen a day.
Cherry blossom - sorry, but you are likely to completely miss it unless you shoe horn in day trips (probably easiest from Tokyo)
There is no way of knowing where you would need to go exactly to catch the blossoms right now. I’d recommend Matsumoto as a likely possibility.
Ryokan stay? Perhaps you’ve identified a place in Hakone you like and can afford. I would suggest not trying in Kyoto, not unless money is no object and you’re happy to pay the significant premium the ryokan in Kyoto fantasy commands.
Do be careful of making non-refundable bookings or somehow ensure you have appropriate insurance. The situation is currently extremely volatile and you may find yourself in the position I am (and many others are) in where there is no certainty that you will be able to or allowed to enter Japan this April (or by doing so face a lengthy quarantine in your country upon your return).
Am happy to help with details, but figuring out what to do is up to you. I’m not a concierge and don’t miss the time my own child couldn’t use cutlery to want to spoon feed anybody else.