Long Itinerary - 60+ days

Wow! Thanks for the information!
In the end I decided to change Yakushima according to your suggestions:
Day 38: Train to Himeji, enjoying the castle, and continuing to Hiroshima
Day 39: Miyajima
Day 40: Train to Kagoshima, and enjoying the city a bit before departing on Ferry Hibscus to Yakushima
Day 41: Tour A, sleeping at Onoaida area
Day 42: Tour B, get back to Anbu around 1300, and go to Oku no Taki, then take the last bus back to Miyanoura
Day 43: Taking the Hibiscus ferry in the morning back to Kagoshima, and a train to Kumamoto

This way I get to enjoy Yakushima a lot more properly! I wanted a hike to the old cedar woods, but didn't have enough days.

Sounds good. I decided not to do the "B" course and head back early because my calves were sore from hiking in the "A" course. We did go and visit the Yayoisugi Cedar while visiting Shiratani Unsuikyo, so you will get to see that one.

I differ from your plan in that I am going up the eastern side of Kyushu. I am currently in Miyazaki, and about to go to the Udo Shrine and Aoshima Island. Tomorrow I will head up to Nobeoka by train, and then take a bus to Takachiho for the night. I then will take the bus back to Nobeoka and train to Beppu.

Even though I have a JR Pass, I seem to be spending a lot of time on busses. I was planning on using a SunQ bus pass for this section of my trip, however, suspension of daily bus services from Koyasan to Tanabe made it more cost effective to get more than a one week JR Pass.

There are too many choices, so little time.