I remember one person here about a year or so ago who asked a question about a ferry back from Kyushu. He/she did a long ride through Japan. Not sure if there was a link to a blog.
Maybe there are also other people like me out there that kept a blog about their tour through Japan.
For me it took about 3 months (but I was working as well) to organize my entire trip). So Kyushu alone maybe you can research a lot in about 4 weeks.
If you read some Japanese you could search for https:九州自転車一周
A few things come up but nothing too detailed.
What worked for me was:
- decide on the places I want to go
- check if there are mountains in between (that would be a no go for me)
- check with google maps on alternative transport
- know that a lot of rivers have “cycling lanes” along them
- know that in rice paddies and other agricultural landscapes you’ll often find small roads that run parallel to bigger ones
- get a Garmin and plan out the rides each day but choosing manually the smaller roads or the ways with less elevation. This was for sure the most important tool I used.
- have a general plan, but make the detailed plan on the go
Note that I stayed on hotels ( not enjoying camping) and always reserved the day before. Sometimes earlier.
As you said you have never done a ride like that, I personally would start with a few weekends or 1 week, just to get a feeling about the equipment you really need, how far each day you can reasonably ride...
There are also (in Japanese) some cycling books with day tours. I have a few for Kanto area. I found them at yroads.
The webpage of KANcycling has also quite some tips. http://kancycling.com/KANcycling/Welcome_to_KANcycling%21.html
In the end, it’s about getting to go. Japan isn’t like the Netherlands but it is still a cycle friendly country.