Upvote:4
You will need to fill two copies of ТД-6 (not a kaomoji) paper on entrance and two copies of same ТД-6 paper on exit. You can google for PDF. Of course it's in russian.
There is non-zero chance you get rejected without any reason, so you need to be prepared to do something in such case.
IMHO it would be more reliable if you do it through some company that has their people on both sides Japan and Russia. So you could talk personally in Japan and get help in Russia. Should be not that hard to find in Tottori. Maybe even DBS Ferry itself can help.