I started a new thread and moved some posts, as this debate (?) was getting off the Sakhalin ferry topic!
Regarding getting in and out of Tokyo:
Even if you are on a budget, I recommend taking the expressway (toll road). Taking surface roads, you really can spend 2 hours in stop and go traffic before you reach somewhere you can ride more than 5 minutes before hitting the next red traffic light. 1 to 15 dollars worth of tolls will get you far enough away that you are moving more than you are stopped.
The Metropolitan Expressway at the center of Tokyo, however, can be confusing as hell. Even being able to read and write Japanese, I sometimes get confused as to where I am going! And there are very few places to pull over and check the map there.
Routes in Japan to avoid include Highway 1 between Tokyo and Nagoya: Traffic is hell and there ain't a whole lot to see. Highway 6 on the Pacific coast is probably in bad shape as there was a bit of a tsunami last year (understatement of the decade?). Going to or from Hokkaido, don't ride the entire way on Highway 7 on the Sea of Japan (that would be East Sea to you Joe!:confused1  : the scenery is mostly the same all the way.
Disclaimer: The opinions above are my own and may or may not reflect the real situation or tastes of anyone other than myself.
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