Hey all,
I used to work at a private university in Japan processing MEXT applications (Embassy and University). I can't really talk about the Embassy interview phase, which is where it sounds like most posters here are, but once you pass the Primary Screening, I've written up a guide based on my experience at the receiving end, for what it's worth:
MEXT Scholarship (Embassy) | TranSenz: Expat Living in Japan
I see from some of the posts here that a lot of you had to submit your university and professor choices ahead of time, a requirement that varies from country to country, but I wanted to chime in on the discussion about private university placement on the previous page. I was at a large, private university away from Tokyo and about 20% of the students we issued letters of acceptance to ended up coming to us. Almost all of our applicants had us as first or second choice. 30% MEXT scholars being placed in private universities is a pretty small number if it's true, since about 80% of universities here are private, but it is possible.
For the university application process, we wouldn't talk to applicants until after they had passed the primary screening. As hard as everyone's working for the Embassy screening though, keep in mind that none of that carries through. There's no communication between embassies and universities so when you hit the university, you're starting from scratch again and the Research Proposal is everything.
I don't handle applications anymore (so there's no conflict of interest), but I'd be happy to answer follow-up questions on the blog post above (sorry, but I don't think I'm going to be able to keep pace with this thread).
Anyhow, best of luck to everyone!