1 month trip, Yakushima to Kamikochi, doable?

Hello friends, any help/suggestions would be greatly appreciated. Prior to this trip, I will be spending two weeks traveling the common route of Tokyo/Kyoto/Osaka/Hiroshima with someone and then will be staying in the country for another 4 weeks by myself. I have been working on the rough itinerary of this part of the trip for a couple weeks now but would like to start booking accommodations as it is right around the corner. I did not plan the trip around a 21 JR pass but after asking for advice on another forum I was told this would be my best bet. I do not mind the longer travel times on some days as I will have school work (unsure how demanding it will be at this time) to complete during the trip so I figured this would give me some down time to work on it. I am interested in hiking, nature, and good food for the most part, but am always open to suggestions. Yakushima has always been a dream of mine so unfortunately I will have to deal with whatever the weather throws at me, and am okay with that. I'm also looking for suggestions for a day trip or overnight between Fukuoka and Nagoya to possibly split the travel time between two days (was thinking of an overnight near Ominichi so I could do the shimanami kaido ride. Still have A LOT to research/work out but again just looking to book my accommodations before it gets too pricey. Thank you for reading!

5/27 SUN - Fly from Tokyo to Kagoshima, night in Kagoshima
5/28 MON – Half day in Kagoshima, overnight ferry to Yakushima @ 1800
5/29 TUE - Arrive Yakushima @ 0700, stay Yakushima, Find hike/something to do
5/30 WED - Stay Yakushima, do Shirantani
5/31 THU - Stay Yakushima, do Yakusugi Land
6/1 FRI - Early/fast ferry to Kagoshima or possibly Ibusuki? Half day in either, stay Kagoshima
6/2 SAT - Stay Kagoshima
6/3 SUN – Start JR pass - leave Kagoshima, go Miyazaki (144 min) Stay Miyazaki
6/4 MON - Stay Miyazaki
6/5 TUE – Leave Miyazaki, train to Nobeoka/bus to Takachiho (160 min) Stay Takachiho
6/6 WED – Half day Takachiho, bus to Kumamoto (180 min), train to Nagasaki(154 min), stay Nagasaki
6/7 THU – Stay Nagasaki
6/8 FRI - Train to Fukuoka (120 min), stay Fukuoka, dinner with family
6/9 SAT - Stay Fukuoka, family time/ do ????
6/10 SUN - Stay Fukuoka, family time/ do ????
6/11 MON – Stay Fukuoka, family time/ do ????
6/12 TUE - Leave Fukuoka, go to Nagoya (266 min), half day Nagoya, stay Nagoya
6/13 WED - Gujo Hachiman day trip, Stay in Nagoya
6/14 THU – Leave Nagoya, Kiso Valley half day trip? Train/bus to Magome (80 min), walk to Tsumago, train to Matsumoto (107 min), stay in Matsumoto
6/15 FRI – Leave Matsumoto, travel to Kamikochi (90 min), stay Kamikochi
6/16 SAT – Stay Kamikochi
6/17 SUN – Leave Kamikochi, go to Takayama (85 min), stay Takayama or Hirayu Onsen area
6/18 MON – Stay Takayama
6/19 TUE – Leave Takayama, head to Nikko (356 min), stay Nikko
6/20 WED – Stay Nikko
6/21 THU – Leave Nikko, travel to Hakone (180 min), stay Hakone
6/22 FRI – Leave Hakone, go to Tokyo (108 min), stay Tokyo
6/23 SAT – Last day of JR pass, stay Tokyo
6/24 SUN – Stay Tokyo
6/25 MON – Stay Tokyo, Leave Tokyo

You might be traveling right at the front line of the rainy season for most part of your journey. As you are traveling alone and if you are okay on a few changes along the way I would leave it very flexible so you can travel according to the weather. Actually your better bet might be to do the trip in the opposite direction. Start North, go South.

I did a 2 months cycle trip through Japan last year and booked accommodation only the day or 2-3 days before, allowing for flexibility. I found that Jalan was the best source for booking accommodation. While for major cities I found Toyoko Inn practical. But they do book out quickly. They have a good discount scheme.

I really liked the Shimanami Kaido. If youfd like to take a look:
http://bicycletraveljapan.blogspot.nl/2017/11/part-10-day-48-49-riding...

Enjoy your trip to Japan!

Thank you so much for your reply! I'm curious as to why you advise to start north and work my way south rather than starting with Yakushima first. I figured with how heavy the rain is in June that it would be better to get down there as soon as possible. And thank you for the Jalan website tip, did you find that booking last minute was more expensive? I'm trying to average around $50 a night for accommodations currently and figured my only last minute options were manga cafes and capsule hotels.

Rainy season as Sakura and koyo cannot be predicted accurately. BUT rainy season starts in the South and goes up North. So Ifd figure that if you travel in the same direction you have two possibilities:
A) you are lucky and always traveling a few days ahead of the rain.
B) unlucky and traveling under the rain for 5 weeks

If you go North South your chances might be higher to just cross the rain once (for a few days) and then be too much in the South so it already stopped.

But I would say my main advice is to leave it flexible.

For room rates, I actually donft know. As I didnft compare to earlier booking prices nor did I really need to manage a budget.
It might be more a problem that certain accommodations got already sold out. But with a bicycle you are much less flexible than by train/plane.
However traveling alone means you pay more for accommodation than traveling in two.

Also on Jalan you get points that pay for real money for upcoming reservations. BUT I think you only get your points at the end of each month. So for the last few nights you might be able to get a discount.