To throw something in here...
While you're figuring out the practical aspects of your plan, read as many books as you can written by people who've done motorbike touring - it doesn't matter whether it was in Japan or not.
About Japan, you can learn facts from the internet, books etc., like people have been assisting with here.
About the actual touring itself - research it and learn from other people's experiences.

Personally, I have never done motorbike touring. However, I
have toured a lot on a pedal-bike. I clearly remember making the preparations for my first 'expedition'. ^^ It's surprising how much you can learn at 'second-hand'.

I hope you go with your second feeling and choose a bike designed for touring. They are designed that way for a reason.
Also, it's a bad idea to carry all your luggage on your back. It's hella uncomfortable!

It's bad enough on a pedal-bike, where the handlebars allow you to shift position slightly - I can't imagine how bad it must feel on a motorbike, when you can't change your angle, and you need to use more strength to steer. So it's better to find other ways to carry your stuff!
I'll shut up now.

Good luck!
