How much motor traffic did you meet on those roads, and how courteous were the drivers?
Once I was away from the larger urban areas, I was mostly able to plot a course that avoided the busier roads. There are a lot of roads to choose from. Sometimes it was a balancing act, because getting off the main highway meant meandering through a maze of back alleys with stop signs every block, or climbing a hundred meters up a 20% slope to avoid the highway following the river valley. A lot of times though, even on the main road there would only be a one car passing every couple of minutes. I would say in 26 days of riding there were only about 30km where I thought to myself “this sucks”.
The level of courtesy shown by Japanese drivers is almost incomprehensible to someone coming from North America. On the few occasions that my route planning was less than stellar and I found myself on the side of a busy, shoulderless highway, I was never passed “too close for comfort”. Most cars were small enough to pass without crossing the centre line, although most moved over when possible. Every one of the trucks would wait patiently for a break in oncoming traffic to give me a wide berth, even when I was grinding uphill at 6km/h. Leaving Kagoshima, on a particularly busy stretch, trucks would be stuck behind me for a minute or more before there was a break, or I could find a place to pull off and let them pass. No horns, no crowding, no drama, just patiently waiting. I always gave them a thank you wave, which was always returned with a friendly tap of the horn.
Japan also has a 60km/h highway speed limit everywhere but on limited access expressways where bikes are forbidden. Even though this seems to be a “guideline” rather than a rule, it meant even on highways most vehicles were going 70ish, compared to here in Canada and USA where everyone on two lane highways passes at 100 to 120 without slowing down or moving over.