Today, I got an email from the university, saying they have reserved my place in waseda but must wait for embassy to inform me.
So finally, I am back on the track. After 4 months, the waiting was driving me nuts , I couldn't work or even study. Now that I got accepted, I will be more ambitous about everything.
By the way, Jpstw, the requirements of the scholarship depends on which type of scholarship you applied; undergraduate student or research student. Best way to learn the requirements and the procedures for monbukagakusho is to call the japanese embassy/consulate in your own country.