My last trip to Japan, I brought my Brompton. When I arrived, I went to a delivery service (Yamoto) in the airport and had the bike delivered to where I was staying. This saves the grief of dragging it onto subways etc. Even when I flew between cities I have my bike delivered. I rode all around Osaka and Tokyo. I also did a day trip to Sakai City Shimano Bike Museum.
If you take a bike on the
Shinkansen it must be bagged and rinko'd and you must make a reservation for your bike. There is a limited space on these trains so keep that in mind.
When in the big cities I used Kamoot to plan my routes but I use the filter of quiet roads. This will take you through neighbourhoods you would never see by subway. This made riding so much fun. In Tokyo you can rent bikes and even ebikes that are like bike share bikes.
I have done Shimanami Kaido but I rented a bike when I was there. It was a great trip and well worth it. If you go at a slow pace anyone can do it. Though be forewarned, the ramps onto the bridges can be tiring. Mini mountains. Some cities in Japan are un-ridable. Nagasaki for one. The hills are just too big. Even in Onomichi proper, the hills are incredible. Also people think Tokyo is flat but it is far from flat. Japan is mountains and ocean (some volcanoes). I have ridden the mountains, it was extremely hard and don't try this in the summer, it is too hot. I have done rides a long the coast, again with rentals which have been great.
My advice for a first trip to Japan with others who are not cyclists, I would leave the bike at home and enjoy a non-cycling holiday. If you have to ride then renting is the easiest solution.
Blue Lug in Tokyo is a treat and so is Grand Bois in Kyoto. Loro cycle for Brompton, especially in Osaka is fun to go to.
I have been to Japan at least 20 times and last month was the first time I brought my Brompton. The only way I would bring my Rivendell is if I was staying at least a month and cycling was the only thing I intended to do.
Have fun.