Actually, I sent the final draft of my essay (Field of Study and Study Program) to my professor that's why he contacted me. In my case, they asked me to send 2 sets of application, one for my university and the other is for MEXT. The have different requirements.
I've sent the first set and I'm already working on the second.
By the way, the student support office also informed me that they received my toefl official score certificate last Jan. 30. It was sent last Jan.8 from the toefl office. So I guess it takes 3weeks to get to the university. Funny thing is, I haven't received my own copy yet.