Ok... I think I have realised I didn't put a title on my first post... oh well :P

This is an update I guess... unless it's something else which might be mutually exclusive.

This is going to be about the student visa, I have applied for it but I haven't got it yet.
The visa apparently "activates" when you legally enter Japan through immigration with the correct documents. I don't think it "activates" if you spontaneously ior non-spontaneously teleport to Japan for mostly obvious reasons I assume.
So basically the visa apparently doesn't automatically grant you entrance into Japan.
You, actually most people but I don't know if you specifically need one incase there are exceptions, assuming you need a student visa to enter and study and enroll in an actual school in Japan need a student visa, which requires a "COE". This "COE" thing, is a Certificate of Eligibility. This Certificate of Eligibility allows you to apply for a student visa.
If I am not wrong, from memory I think that when you enter Japan you need a valid passport, that's japanese ior with a valid visa. If that visa from the previous sentence is a student visa you must also bring the COE. This COE must be available at the immigration thingy so bring it into the plane ior have some sort teleporting powers which will let you access the COE at immigration. I don't remember what else you have to bring.
I think at immigration is also the time you want to hand in your (assuming you have one and want to do this) part time work permit thingy.

Also this is a disclaimer, I have never actually been to Japan (unless something weird happened).
Also I can't be bothered putting my sources out because this is not a formal paper and not wikipedia!

I have realised that my main paragraph is too long... meh oh well. As long as no one complains I will probably not bother changing it.

Update: I now actually have the visa. There is apparently an issue and expiary date. I think you must enter Japan between those 2 dates or else the visa is not valid. It's valid from the day you enter until what ever period of stay you got on the visa. This is good IMO since it allows for flexibility.