1. When it says (original 1, copy 2) next to the document, does that mean we need to send the original document AND 2 copies of it, or is that in a sense; 1 original document OR 2 copies.
One original document + 2 copies of the document .
Here the exception for us was the graduation certificate. Didnot submit the original but an "attested" copy.
This depends on the Embassy, so, not sure if this will be the same for you.
The letter of recommendation from the Dean
For Embassy recommendation, it can be from any supervising professor.
Also, is it better to use a free format or the available sample
You will get a "recommendation form" (Google it, MEXT recommendation form, it might still be available on some Embassy pages)
I'm having a bit trouble with this because in my Uni we don't really have close relationships with our professors and especially the Dean, so asking them to evaluate my "interpersonal skills" or "self-confidence" is a bit ridiculous since they don't know me. We don't have a personal student adviser, either
I'm sure the dean or any professor has probably written a letter of recommendation for atleast one student.
When its a free format, usually, you write the recommendation,get it checked by your supervising professor(or the supervising professor writes it) and then get the dean's signature.
Its a relatively easy form so you dont have to fill in anything. Talk with a friendly professor or a senior and ask how you should go about getting this recommendation.
This will probably help you if they insist on a free format recommendation letter.
If they ask you to get the recommendation form they provide you with, you dont have to follow those instructions.
Remember, those guidelines are for university recommendation where you absolutely need to have a recommendation from the dean. For embassy recommendation, a recommendation from a professor works.
about this confidential envelope
Get a normal envelope and write "confidential" on it. Address it to yourself.
the Dean needs to sign on the envelope where it's sealed
Yes.
For filling in the application form use
this. Forms for Embassy and university recommendation are almost similar. (Remember I said ALMOST )