In 2018 we visited Japan and cycled around for 3 weeks. Japan is a really friendly for cycling. Camping is safe and surprisingly easy for such a highly populated country, convenience stores are everywhere providing food, drinks, toilets and charging. There are hot springs around every corner and vending machines with both cold and hot drinks in random places.
Just try to avoid taking your bicycles on trains. Doable, but more stressful than it should be.