What is the best mode of travel , also budget wise to travel the following route

We will visit Japan from 17 October till 06 November 2025, we arrive in Tokyo and depart from Fukuoka
We will spend 2-3 days in each destination : our itenary is as follows:

Tokyo > Takayama > Kyoto > Onomichi by bike to Imabari > Hiroshima > Beppu > Fukuoka

I am looking forward to your reply.

Kind regards,
Jolanda