I am not doing as long of a trip as you are, but we overlap in a few places. I leave in two days, and I can try to give you some feedback if you need it.
I am going to give you some ideas as to what I am planning to do.
You plan to visit Yakyshima Island, and I am also planning to do that. My original plan was to use the Ferry Hibiscus, but I was not able to get information about what happens when you dock at Tenekashima Island at 9PM. You may have to disembark and get a hotel, and then return before 5:30AM, when the ferry leaves. I've decided to do the roundtrip jetfoil ferry route.
I am also not going to rent a car, and do the two day bus tour (A & B). depending on when you can get to your hotel on the day 42, you may not be on time to do the all day "A" tour, but will have to do the afternoon "C" tour.
Yakushima bus map and schedules:
http://www.scribd.com/doc/103326219/Bus-map-and-free-passThe "B" tour ends at 1:15PM, and you will have to take the jetfoil ferry back to Kagoshima.
I am also going to visit Koyasan and then go to the Kumano region (yours days 47-51) . I was orininally going to get a three day Kansei Wakayama pass, and use it to go to Koyasan and the three temples in the Kumano area, Nachi Taishia, Hongu Taisha, and Hayatama Taishia.
My original plan was to vist Koyasan on the first day, go to Tanabe by bus on the second, and visit the three temples on the third by bus, and take the train back to Tanabe. This is do-able, and will cost less. It also looks like the bus service from Koyasan to Tanabe is weekends only, So since I am planning on doing this on May 7th (a Tuesday), I had to change my plans. I now have an active JR Pass while I an traveling in the Kumano region.
Link to English KW Pass and bus timetables:
http://tb-kumano-news.blogspot.com/2012/03/new-kansai-wakayama-pass-w-...After looking at the cost for the tickets, I decided to get a two day Koyasan World Heritage pass, and use a JR pass on the second day to stay in Katsuura at a hot springs resort. If I feel like seeing one of the temples that day, I will take the train to Shingu, and see Hayatama Taisha.
On the third day (your 49th), I intend to activate a two day Kansei Wakayama pass, and go to Hongu Taisha and Nachi Taisha. If you plan to stay at any of the onsens near Hongu Taisha, I would recommend going this route. I plan to spend that evening to Shirahama and stay in a beach hot springs resort, and use the second day of the pass to get around Shirahama and possibly go to Ryujin Onsen or Takahara, before leaving the area. Your plan looks like you could also buy both pass like I am planning.
I would also like to add that Shirahama has nightly fireworks each evening, but they have a massive fireworks display (two and a half hours) on August 10th, so if your plans make it possible to be there at that time, there are still some hotel rooms in Tanabe, which is close to Shirahama, and the KW Pass can be used for the Tanabe-Shirahama beach bus, which makes about 30 round trips a day.
I hope this helps.