This [1] is more of less what I did. There wasn't much of any dedicated cycling lanes (such as the Shimanami Kaido road) anywhere I went, so sometimes the traffic was not so cool.
The parts in and out of the Alps, and in Mie prefecture (despite the off-road garbage ;) were the best to me: no so much traffic, few people, and the scenery was quite cool. My time was short and there were several places I wanted to connect, so YMMV.
I did 6 times but weather was a bit crap and many places were already closed (and I really needed that shower at the end of the day :p). On the other end, I was practically alone most of the time (I shared a barbecue under a tarp under the rain with a Japanese guy on my last camping day) and most of the camp sites were just by the sea, which was pretty cool.
[1] https://drive.google.com/open?id=1nuRT79jhVqLFPncCh9PnUhxK6K...