So far essentially I have been using the following resources to plan my bicycle tours:
Surf around the internet and try to find an actual bicycle road, described by someone else already. In many cases this will be again along a river. But there are some others, like Tsukuba Rin Rin Road, the cycle lane heading West from Enoshima or the ones the MLIT published on their web page.
Check out the routes in the Jitensha Sanpo (自転車散歩) series of books. You need to be able to read some Japanese, but they have maps, elevation profiles and pictures, so many things are quite self-explanatory.
Well, and since I have my little Garmin, I also just simply check out on Google maps a location that would possibly interest me (and be flat enough for me to handle) and see what Garmin comes up as a route. I haven't yet found a way to let my Garmin know that I prefer the really small streets. So it always goes for the bigger ones, so I then manually drag the route over to smaller ones. Sometimes this however makes that I end up in non asphalted streets, which isn't good either and ofter a reason to change the route along the way.
Or use Komoot for the same purpose. Komoot is definitely coming up with better routes, however it doesn't come for free. (I haven't used komoot at all during my 2 months trip through Japan, as I only discovered it later in the Netherlands and really only started using it in 2019).
- Find a river in Google maps and check if it seems to have a small road running alongside.
- Also see this post on cycle roads in Japan, mostly along rivers: Bicycle roads in Japan
- Some other examples of finds in the wide wide web: