[sarasi]

Hmm. Accommodation is limited in Yakushima, especially in the budget range, and getting around without a car is not easy, so I strongly recommend booking the youth hostel in advance. You would be in a bad situation if you arrived and found the youth hostel was full, and that kind of thing happens often in Japan. April is a popular time to visit Yakushima as well.

The Tokyo-Nagoya leg is definitely covered by the JR pass.