I cycled in Japan in April for 2 weeks, starting in Hiroshima and covering the southern 2 islands. My son was cycling for 3 months seeing the entire country and this is the part I joined him on. We used motorcycle map books to plan our route which worked out well. Cycle touring isn't a well known concept there, most people just ride utilitarian bikes to work, market and school or they are performance/racers call 'pro bikers'. Japan tends to be either flat or mountains, no real in between.
I was a real novelty, being the mother of a 23 yr old and riding self contained. When people found out we were a mother/son trip they were always amazed, admired the generations enjoying each other (their generation relationships are similar to the US in the 60s) and my son loved telling them that I was 52 yrs old, which no one believed (helmet covers the gray!).
We camped by the side of the road, in camp grounds, stayed in hostels and one night in a hotel. We took trains into sizable cities when the traffic got too much, which was never easy for me as you are required to put your bike in a bag and carrying it w/the wheels removed along with panniers was hard. My son had a Bike Friday folding bike and his smaller bike bag had straps that he could carry on his back.
We had a lovely time--exotic yet modern in interesting combinations. People generally were very gentle and friendly. Maybe they are different in the crowded big cities, and drivers were very curteous.