I participated with my local bicycle club in the
Shimanami Kaido event back in 2016, which was their "small" event (approx. 3000 participants), while 2018 was their "large" event (8000 participants). Spectacular to say the least! It is a definite bicycle tour bucket list. It's Japan's premier bicycle route, so you won't be disappointed. The main difference between the event and doing on your own, is that during the event, they close off the bridges from motor vehicles (both directions), so it was very peaceful biking with thousands of other cyclists during the event on the bridges over the ocean. They even had locals come out to cheer for you along the roadside. Unforgettable!
Since you'll be doing this at your own pace, just enjoy the scenery and small quaint towns along the way, but
most definitely at the end of the day from your rides, make sure you soak in an onsen (natural, hot spring). You'll be rejuvenated for the next day's ride for sure!
Also, in 2018 I participated in an
Eroica event in the hills of Agatsuma/Gunma, at a famous onsen resort. Too spoiled...
(Sigh!...) I love Japan & can't wait until my next bicycle adventure there.
Enjoy your Japan bicycle tour! ALOHA!!!