Thanks for the advice Nyororin. I gave the school my documents last week, so included in that was the passport, so since they needed it, and didn't just scan it, I'm assuming the stamp was put in...However, it looks like I need to ask them to give it back to me with the stamp in it, as they still have it. I'm not 100% sure if they just have it, or if it was mailed off with the rest of the documents...
I'll ask tomorrow...but the stamp thing would save my life. As it is, I'll go either to the Immigration Office tomorrow, or the local ward, and see what they recommend, after confirming with the school.
I don't want to get deported, so I'll definitely be going through the routine, lol...
すみません、すみません…本当にすみません…