I think I help a little.
1) If you are not going to ride across the old USSR you may want to think about sending your bike back home. The price of shipping to Japan then back home may be a lot more than renting a bike for a few weeks or so in Japan. I have not looked but I am betting a cheap bike to ride where ever you want to then ship it home (even if it never gets there) and a cheap bike in japan and sell it there may run less than shipping your bike half around the world 2 times.
2) Have you priced out the amount your going to spend and on what Japan is not cheap.
3) To get your bike back you will need to fly it home that can be the price of the bike right there.
4) I most cops will be fine but some will say you are speeding when you are not and want you pay the "fee" it is a bribe all around the world. It will go like "you are speeding pay a huge fee now or go to jail" you talk give them a smoke or two then you pay a small fee or no fee and you go on your way. Scares the hell out of you first few times, guns yelling pointing all to scare you in to paying. A big smile and quick "smoke?" sets most cops back.
5) You can make this trip work many people have even with a 50cc. but no trip this long will work out the way you plan it. you can not plan every thing.
6) Calm down going crazy will not help you.
5) That said with all the planing you need to do to make your self feel safe you have left your self little time and even less time to come up with a "plan B" like have savings acount with the money to get you home if you fail, get hurt, are gust get sick of riding.
8) get a full motorcycle licence if it good for you in your home it will be good where ever you ride.
9) paper work have it and have back ups and have back ups at home that you have sent to you and if you can fave them backed up on a webpage someplace.
10) go to HU meeting you will meet people that can help and have done trips like tha one you are looking to do.
some web pages for you to look at that will help with your trip.
get to a meeting here is the link
http://www.horizonsunlimited.com/meetings/
Someone that done it 2 times on bikes no one else did.
The WRONG Way Round.... on a Chopper! - ADVrider
The train you are looking at
Russia / Exploring Siberia / The Trans-Siberian Railway
How to plan & book a journey on the Trans-Siberian Railway
got big bucks?
MIR Corporation - 23 Years of Travel Planning Expertise
Japan
Tourism Offices Worldwide Directory
but unlike many people here I do not think there is much problims in getting a bike on a train. It has been done.
The WRONG Way Round.... on a Chopper! - Page 54 - ADVrider