If you've already been accepted on a master's course, you will start directly on it without a research student stage.
I'm not sure I understand your question about the stipend... MEXT pay for the research student stage as well, they just pay a tiny bit less per month. But you will start as a master's student and therefore get paid as a master's student.
JAPANESE GOVERNMENT (MONBUKAGAKUSHO:MEXT)SCHOLARSHIP FOR 2015(RESEARCH STUDENTS):文部科学省
Since you're not in Japan I don't think you need to act like you are. Give a polite smile, say "Good morning, I'm ---- " or similar and shake their hand if they offer it to you. Wait until they invite you to sit down before sitting.
If you're freaking out, try looking up advice for job interviews online - there's tons of advice and nearly all of it is applicable to a scholarship interview.