23 day Itinerary for first time

Hey everyone, I'm heading to Japan for the first time from January 31st to February 23rd, and I could use some advice on my itinerary. I'm traveling on a low-budget, so I’m planning to get the JR Pass to make it easier to move between cities, especially if I change plans mid-trip and it seems that it will pay-off.
I’m more interested in Japanese culture and anime, so I'm skipping the usual tourist spots like Disneyland and Universal Studios. Most of my itinerary is set, but I’m a bit stuck on the middle part where I want to visit Takayama, Yamanouchi, and Kanazawa.
I’m considering two options:
Option A: Spend one night in each city, but I’m not sure if that leaves enough time to visit Shirakawa-go and Suwa-shi in Nagano.
Option B: Spend around 1.5 days in both Takayama and Yamanouchi, and try to fit in Shirakawa-go and Suwa-shi.
Any advice on how to best organize this part of the trip would be really helpful. Here’s the rest of my itinerary:
31/1 - 5/2: Osaka (with day trips to Himeji and Hiroshima & Miyajima)
6/2 - 13/2: Tokyo (with day trips to Hakone, Kamakura, and Kawagoe)
14/2 - 16/2 ????
17/2 - 22/2: Kyoto (with day trips to Tottori (For the Detective Conan town) and Nara)
23/2 Kyoto > Kansai Airport

If the reason for visiting Yamanouchi is the snow monkey park, I'd probably leave Tokyo in the early morning for Nagano and spend the night at Suwa-shi. Then next day to Takayama and Shirakawago. Spend another night in Kanazawa before heading to Kyoto. So that means one less day in Kyoto.
Feb is the plum blossom season. You can visit a couple of plum blossom spots in Kyoto.
https://visitjapan-vegetarian.com/the-best-guide-to-kyoto-prefectures-...

Fitting all of them in 3 nights, you will spend too much time travelling. I would suggest to skip Suwa.

14/2 Tokyo -> Yamanouchi - You can stay around there or Nagano station or Shiga Kogen if you want some ski
15/2 Yamanouchi -> Kanazawa
16/2 Kanazawa -> Shirakawago -> Takayama

Thank both of you,
Yeah mostly is for the monkeys but I would like to bath in Onsen with the snow.
I was thinking about skipping Kanazawa mostly and I really would like to go to Suwa because I'm a big fan of Kimi no na wa

Some of your day trips don’t make a lot of sense for example Osaka with day trips to Himeji, Hiroshima, and Miyajima … are these three separate day trips?? Why not just do on overnight trip staying in Hiroshima or Miyajima on first day travel to Himeji see the castle then continue to Hiroshima stay the night next morning visit Miyajima then return to Osaka …. Nara is best done en route to Kyoto from Osaka or vice versa.

You don't give your full itinerary, but the JR Pass looks like a big financial mistake so far. You could however get a Kansai-Hiroshima Pass and do quite nicely with it. If you can do so, an overnight at Hiroshima is much better. A day for the city and a day at Miyajima is much better. The city has much more than just the Peace Park.
A day trip from Kyoto to Nara is quite easy, in fact, you could stop at Uji along the way if you like. But Kyoto to Tottori one way is nearly 3½ hours one way, so 7 hours of your day just sitting on trains -- you should rethink your plans, or rearrange things like taking a cheap tourist airfare on ANA directly between Tottori and Tokyo.

Some of your day trips don’t make a lot of sense for example Osaka with day trips to Himeji, Hiroshima, and Miyajima … are these three separate day trips?? Why not just do on overnight trip staying in Hiroshima or Miyajima on first day travel to Himeji see the castle then continue to Hiroshima stay the night next morning visit Miyajima then return to Osaka …. Nara is best done en route to Kyoto from Osaka or vice versa.