Roads
Roads tend to me smooth and easy to ride. As a general rule avoiding the one and two digit national roads (upside down rounded triangle signs) can help avoid the busier roads. With speed limits under 60 virtually every road is cyclable.
In recent years there have been an increasing number of by-pass roads which cyclists can’t use
Tunnels
With all the mountains, Japan has quite a few tunnels, some of which can be quite long.
Having a light to ride through tunnels is essential, especially on the back to ensure that one is seen. Riding on the extremely left side of the roadway
Sleeping
Camping
Japan has a reasonable number of camping sites, however many them tend to be car oriented. Most can accomodate a walk-in cyclists. Family camping season tends to be July and August so outside of those months many can be quite empty.
Wild Camping
As a general rule in Japan, if one does not put up a tent, one can sleep just about anywhere that isn’t obviously private property and is pretty unlikely to be given any trouble.
Hotels
Many cites have “business hotels” that can be reservered on travel websites quite easily and outside of big travel seasons are unlikely to be full so city hotels can generally be reserved the day
Wild Camping
So long as one doesn’t put up a tent, one can sleep just about anywhere in Japan without worry for getting in trouble with police or worry for their personal safety.
Food
With the density of towns and villages in Japan it’s hard to get far away from food without trying hard riding in the mountains. Virtually every city has a supermarket and convience stores are peppered along major routes and in virtually every village
Toilet / Water
Toilets are very easy to come by in Japan. As with above, just about every convenience store has a toilet which can be used to refill water bottles
Many parks also have free toilets that are kept in good condition.
Touring in Europe, once of the difficulties can be finding toilets however, this is virtually never a worry in Japan
Trash
Japan, with it’s ゴミ持ち帰り (Take your trash home with you) culture, has few garbage cans around and dealing with garbage can be difficult at times. If you stay at a campsite they will usually provide you with a garbage bag (as garbage typically needs to be thrown out in city-specific garage bags)