Google maps is the best way to proceed as a foreigner in Japan.
In the hubs like Tokyo you will have all public transport information you need including the expected pricing.
Be careful while traveling by car though, experience has shown that the google algorithm sometimes takes dangerous shortcuts through sidestreets that can be really narrow in Japan – No place you want to get stuck with a van. Enlarge the map and make your own decisions to continue to the next main road where applicable.
In and around big cities it’s easy to get around with public transport. Best way is to purchase a chargeable card for multiple use.
In the countryside, taking the bus is a nice way to get back to the car when hiking. You pay while leaving the bus.