I take this opportunity to offer some unsolicited advice on running routes at three particularly scenic places.
At Taketomi-jima, the loop around the center of the island covers 3.3 km on the main road. I'd suggest doing that loop, and adding the longer loop that starts on the small road at the harbor. The two loops are shown in the map below.
And why do I advise such a route? Because it, unlike the more widely known center loop, takes one to Kondoi Beach. This advice may come in handy if you ever find yourself at Taketomi.
At Hateruma-jima, there are no stoplights, and few vehicles. One can run past sugar cane fields to the southernmost point on an inhabited island in Japan. If you take the route shown below, you will pass that monument, ocean views, and not much else. The roads are empty, except for a few tourists on their bicycles.
At Kamikochi, I can't recommend any particular route; there are so many trails, in so many directions, that one can choose a different route every day. Any trail along the Azusa River will be relatively easy going. In fact, I found it so easy going that I ran 17 km one afternoon last month.