Thank you. That is essentially what I am looking for, along with information from anyone who has gone through something similar. I have checked the site but I have never had any issue like this before and I was unsure where to call. This will sound silly, but do you know if I contact the immigration bureau or the immigration information center, or somewhere else? The information center says they have had many "wrong calls" made, and I am not sure exactly where my enquiry falls.
I can understand it sounds stupid to accidentally overstay a day, and admittedly it was. Though I am not sure why it feels you think I would knowingly risk the stress I am feeling now for an extra day in Japan rather than just coming back for 90, haha.