The northern Kyushu JR rail pass is a bargain. It will get you to Nagasaki, Beppu, and Kumamoto.
I have just come from Takachiho, and had a great time. It requires bus travel to get there.
http://www.japan-guide.com/e/e8050.htmlIt is golden week, and I am not sure what parts of this are specific to golden week, but I will tell you about my day.
I stored my luggage in one of the bus stations lockers, and went on foot.
I visited Takachiho shrine, and it was very well kept up, with what looked like lots of very old cedar trees around it. There was a shuttle bus to the gourge for 100 yen, and I went to the main gourge area.
It was very festive, many people were renting rowboats into the gourge, but I stayed on the walkways above and took pictures. There were two stocked fishing ponds for people to catch fish, and the fish were gutted and cooked for you by the vendor. There was also a noodle shop operating "noodle streams", called flowing Somen. It was interesting to watch.
http://www.toyohara.com/inaka/somen-e.htm After I took the shuttle bus back to shrine, I walked back to the bus terminal to go to the cave shrine where the sun goddess Amaterasu was supposed to hid herself away. I stopped in the information center accross the street from the bus center to find that they were teached a craft. They were hand carving Magnatamas out of pieces of marble. The kit was 1000 yen, and had everything needed except metal files, which the information center was supplying. I bought a kit, to take home with me, and then grabbed my luggage and took the bus to the Amano Iwato Shrine.
I dropped my bags at the Hana Ryokan (near the shrine), and visited the shrine. After going to the shrine, I went back to my Ryokan, and found out about a free shuttle that eveing to the Yokagura Dances at the Takachiho shrine.
The Ryokan had a 14 course meal. Well fed, I went to the dance all at the shrine.
The Dance hall fee was 700 yen, and the hall showed three of the standard Yokagura dances, and an additional one (a Goshintai Dance) about two gods making Saki and getting plastered. The last dance was the most fun to watch.
The Ryokan supplied free tickets to the Amano Iwato Spa, but I ended up finishing the day at their bath before going to bed.
In all, it was a very full day.
The meal in the morning was just as elaborate, and the people at the Ryokan drove me to the bus station after the breakfast to catch my bus.
If I ever come back to Japan during holy week, I plan to go to Takachiho again.
I am not sure how much of this appeals to you, but I thought it wouln't to mention this as an option.