If you can prove ties and establishment in Japan, my guess is, you should be fine.
But my concern is, you mentioned that you have entered Canada before as a tourist, did you ever have to apply for ETA? I hope you have been 100 percent truthful, at least to your knowledge, about your overstay in the US while filling out the ETA application. If you did not mention about your overstay during your ETA application, then it may count against you for future visa applications.
Also, as everybody here has been saying repeatedly, be truthful to the best of your knowledge, and make sure to mention the overstay in your study permit application.