help with my itinerary

I wanted to ask about my itinerary, I have 2 different routes, one with and one without Kagoshima.
Which one sounds better? Any tip or things that need to be changed to help us finish so that we can start booking the hotels?
Thanks a lot for your time!:)
OPTION A)
S - 28 April Madrid – Tokyo (arrive at 07:00 h.). Night in Tokyo
M - 29 April Tokyo . Night in Tokyo
T - 30 April Tokyo – Kamakura. Night in Tokyo
W - 1 May Tokyo – Cinco Lagos - Night in Tokyo
T - 2 Mayo Tokyo . Night inTokyo
F - 3 May Tokyo – Nikko . JR Pass 14 dias activación. Night in Tokyo
S - 4 May Tokyo – Matsumoto - Takayama . Night in Takayama
S - 5 May Takayama - Shirakawago – Kanazawa – Night in Kanazawa
M - 6 May Kanazawa – Kyoto . Night in Kyoto
T - 7 May Kyoto. Night in Kyoto
W - 8 May Kyoto – Hikone - Night in Kyoto
T - 9 May Kyoto - Night in Kyoto
F - 10 May Kyoto. Night in Kyoto
S - 11 May Kyoto – Koyasan (2.5h)- Miyajima. Night in Miyajima
S - 12 May Miyajima - Hiroshima.Viaje Kaoshima tarde(5h). Night in Kagoshima
M - 13 May Kagoshima Sakurajima volc. Night in Kagoshima
T - 14 May Kagoshima – Osaka (5h). Night in Osaka
W - 15 May Osaka – Nara – Inari?? - Osaka. Night in Osaka
T - 16 May Osaka - Tokyo JR Pass ends. Night in Tokyo
F - 17 May Tokyo. Night in Tokyo
S - 18 May Tokyo. Night in Tokyo
S - 19 May Tokyo – Madrid.
OPTION B)
S - 28 April Madrid – Tokyo (07:00 h.)
M - 29 April Tokyo .
T - 30 April Tokyo – Kamakura. Night in Tokyo.
W - 1 May Tokyo – Mt. Fuji. Hakone o Cinco lagos Night in Tokyo.
T - 2 May Tokyo . Night in Tokyo
F - 3 May Tokyo – Matsumoto - Takayama. Night in Takayama. Inicio JRPASS 14 días
S - 4 May Takayama
S - 5 May Takayama – Shirakawago - Kanazawa. Night in Kanazawa.
M - 6 May Kanazawa – Kyoto (por la noche). Night in Kyoto
T - 7 May Kyoto.
W - 8 May Kyoto. Castillo Hikone. Night in Kyoto.
T - 9 May Kyoto
F - 10 May Kyoto – Nara – ¿Inari?. Night in Kyoto.
S - 11 May Kyoto
S - 12 May Kyoto – Hiroshima – Miyajima. Night in Miyajima.
M - 13 May Miyajima – Osaka. Night in Osaka.
T - 14 May Osaka - Koyasan - Osaka (Tarde/noche). Night in Osaka.
W - 15 May Osaka - Kyoto – Tokyo. Night in Tokyo.
T - 16 May Tokyo – Nikko. Night in Tokyo. Fin JRPASS
F - 17 May Tokyo
S - 18 May Tokyo
S - 19 May Tokyo – Madrid.

Hi. Given the length of the trip i think you should definitely stay for a full day and night in Takayama. It is a real highlight. And worth visiting Magome and Tsumago which are a lovely walk in the Jpn Alps. Also, Kanazawa is great for its famous garden which is worth visiting. From Miyajima and Hiroshima you csn take train and stop at Nagasaki which is intetrsting and half way to Kagoshima. I like Kagoshima with its hot springs and volcanoe but Kirishima Nat Park is also beautiful en route. Good to spend quality time in Kyoto and Tokyo but i think its worth seeing the other places and cutting the odd day at both. Matsumoto Castle is also good near Alps and Kamakura beautiful.

You can conceivably do Koya in a day but I would really recommend that you consider staying a night there. It's a longer trip than you might think.

I'd go with option B!
A sounds more like something I would do, but it's very stressful and you won't be able to explore everything to the fullest. You'll notice that one place has so many other things to see, but you won't have time for them as you have to rush to the next destination.

Kagoshima and Sakurajima are awesome, but I highly recommend coming again and doing a "Kyushu tour" then instead of squeezing it in now.
Kyushu has SO much to offer that it would be a shame to only go to Kagoshima: http://zoomingjapan.com/tag/kyushu/

Unsure if you are interested in seeing sakura in bloom ,HANAMI , which is one of Japan's main attraction.

Late April is too late to see hanami in either Tokyo or Kyoto. But not in Tohoku.
In fact end if April is the best time to view Hanami in Kakunodate , Hirosaki and many other places in Tohoku.