tomayto,
The japanese language course is only necessary to those that need it according to MEXT. this depends on your study field. In case you do need it, i think i read that, whether you enter in either april(24month) or october(18month), your first 6 month will be dedicated to learning japanese. and, i think these 6 months are taken from within the 24/18month period. the earliest to enter is in April(24months). The language courses will not run simultaneously with your graduate/research studies. It might be in a seperate location. I dont really know where you will take the language courses... but i think i remember reading it would be in tokyo or osaka... but dont quote me on that.
clauxz,
I wouldnt called you a "newbie" ha. you're well ahead of most of us here. you should probably be answer our questions. For your question, I think you should first definitely email the department you are applying in and ask for the application process(unless it was already clearly stated, which its most likely not). I think you should always approach the prof first and let them know, then apply through the department. From my experiences, if the prof does not reply, that is a way of saying no, or im too busy. I think in most cases, you need the profs approval first. I know some univ ask you to send in all your monbusho applications and select a supervisor, then maybe they will do their own admissions process. im not really sure... again please ask the department
kayumi,
um, yes, it is possible to enter graduate school for a masters degree with this scholarship... i didnt understand what you wrote from there... sorry.