is a good resource for what you are wanting to do. I did about a 2-month tour last summer, it was a blast. I went from south of Fukuoka up over onto honshu -> shikoku (all around shikoku) then -> kyoto/osaka/nara and surrounding. I used japancycling's website as a general template for what I wanted to do then kind of played it by ear, but having lived there for about 4 years it was a lot easier for me because of having friends all over the place, in other words, YMMV.
how's your japanese? once youre outside of tokyo/osaka its will be a challenge to communicate if you do not have at least some basic command of the language.
"stealth" camping is easy in JP if youre wanting to go this route. I camped in parks, off the side of the road, just basically anywhere I wanted and was never hassled. this is good because youre gonna spend *at least* $40 / us (4000-5000 yen) per night for a hotel.
someone in that other thread recommended youth hostels, but outside of osaka/tokyo they are so spread around and making reservations is such a bloddy hassle (seriously) that it's really not practical to do the hostel thing. I recommend business hotels "Bijinesu hoteru" in katakanized japanese. these are in every moderately sized city and you pay up front, never needing reservations. I stayed in one every 2-3 days just to recharge batteries on portables and have a nice shower. hot springs are all over the countryside, that may be another alternative worth checking out. down side of business hotels is that usually they speak zero english.
in the summer months japan is *really humid* so make sure you have appropriate gear, footwear, etc. this, along with the mountanous terrain, can be very tiring. if there are hills in your area, I suggest practicing on them.
end of June is like, the heart of rainy season. it rains all day, almost every day. it's not like a spring shower either, its like, varying degrees of hardcore rain. if youre dead set on doing this at that time then dress appropriately.
I realize there are a lot of negative comments here, but I'm trying to give you a realistic perspective and your OP isn't greatly detailed as to what youre planning to do. If you update later I can probably give you some better feedback.
Here are the biggest pluses of touring japan:
- outside of osaka/tokyo people are really friendly and interested in random white people riding loaded touring bikes. you *will* be invited to stay the night at some familys home, I can say with 90% certainty. japanese people are really warm and friendly once you get outside the city areas.
- of course the nature and architecture and everything is totally different from what you'd be coming from in any western country, so thats a real trip
- you'll probably see random things every day that will make you say "WOW THATS COOL"
Cheers. If you have any additional comments about the goals of your trip and maybe a bit of background I can provide you with a little more feedback. I spent a lot of time in Japan and have a lot of knowledge in this area.