Need help to plan transportation for 1 month trip

Me and my bf are currently planing our vacation to Japan next month. We are planning to visit 3 different regions and lots of prefectures. Since we dont have much experience with planning trips that big and with travelling in Japan, we have no idea which transportation to consider that isn't too expensive. We also want to save time and not take the cheapest and longest route that will take forever to get to each destination. I tried to do some research but there are so many different passes and different trains, its a bit overwhelming for me.

If you have experience and got any advice or recommendation, please feel free to share it, thank you :)

This is our plan:

July 25

Arrive in Osaka

July 25 – July 27

Stay in Wakayama

July 27 – August 1

Stay in Kyoto

August 1 – August 2

Stay in Kobe

August 2 – August 3

Stay in Himeji

August 3 – August 5

Stay in Hiroshima

August 5 – August 10

Stay in Fukuoka

August 10 – August 13

Stay in Kumamoto

August 13 – August 16

Stay in Miyazaki

August 16 – August 17

Stay in Beppu

August 17 – August 22

Stay in Tokyo

August 22 – August 23

Stay in Yokohama

August 23 – August 24

Stay in Kamakura

August 24 – August 26

Stay in Hakone

August 26 – August 28

Stay in Osaka

August 28

Flight Osaka-Home