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There is a tourist information booth close to each port of entry. They sell bus passes.
Schedule a pickup to have your luggage delivered from one accommodation to another while you explore the island during the day.
Rent rain gear, shoes, and a backpack so you don't have to travel with wet luggage.
For hiking outside of Shiratani Unsuikyo Park and Yakusugiland Park, consider making a one-time donation at an information booth.
All tap water and mountain streams are drinkable.
Consider hiring a guide to make the most of your time.
Crafts and factory tours make for good rainy day activities.
Many businesses close early and buses stop running early, too.
If you're renting a car, don't forget your international permit if needed. There's only one main road around the island, so you shouldn't get too lost, but be aware that just because a street shows up on your GPS map, doesn't mean it's a reliable street to take.
If you're a serious cycler, bring your pedals and check out You Shop and Nangoku in Anbo and Miyanoura. (The owner of You Shop speaks English.)