If they make it to Honshu, I don't think they will do much more than pillage. I think a long term hold on the island is impossible.
Now let's say that they form their fleet at Yongmingcheng (Vladisvostok) and set sail for the island of Hokkaido. Hokkaido was lightly populated and the Yuan could bring those they needed from the mainland to set up permanently. The Ainu may even prefer the Yuan Dynasty to the Japanese, so a small force of indigenous people may work for the Khan.
Gaining a foot hold on the island would now have the remaining Japanese islands in a vice between the Korean Peninsula and Hokkaido. Even if the other islands are never taken, when the Europeans arrive Japan may look for allies in them against the inheretors of the Yuan dynasty.