Just came back from a 7D6N trip to Wakayama Perfecture. All ground arrangement by myself, covering Wakayama City, Kii-Katsura, Nachi, Shirahama, and Shirasaki Kaigan via Japan Railway and bus. Fantastic place and food. Heres some pics in Nachi, which is also on the UNESCO Heritage map
Getting there:
From Wakayama City to Nachi is about 3 hrs ride by JR. Then a 15 min bus ride to the base of Nachi mountains. From there 2 hrs hike through 1,000 year old cobble stones and cedar forest to Nachi Shrine and Nachi Falls. Then 1 km hike down to the nearest bus station and back to Nachi station. Ideal place to stay is at Nanki-Katsura National Park Resort. Rate covers buffet breakfast and dinner and free shuttle from Kii-Katsura Station. You can travel to Nachi Station from Kii-Katsura Station.