I finally returned, so I can respond to some doubts that were posted above.
yudanteiki, I also thank you for writing your experience, and I also agree with all the aspects you mentioned.
"vinculative" might be incorrect English, but with this I mean that the results of the English exam have a direct, unavoidable bearing on the final result of your application.
The result of my Japanese exam, whether I had zero or 100%, would not have a direct influence on my final application result. At best, if two candidates have exactly the same scores in everything, but one has a better result in the Japanese exam, it might potentially be used to weed out the other one, but as far as I have heard from people that work in the embassy but were not directly involved in the selection process, this rarely happens.
But, if you are applying at the embassy for a major in Japanese language, or some field where Japanese proficiency is required, the results of the Japanese exam matter greatly, perhaps as much or more than the English exam.
As for what happens after you arrive in Japan: it is a lottery, and best explained by giving real cases that involved friends of mine who are also MEXT recipients. But in 99% of the cases, you will have to do entrance exams at the university you applied for.
one friend went to Hiroshima University; 8 months before his trip to Japan, he had already been notified by the professor/supervisor that he applied to that he would only be accepted by him as a master student if he undertook the entrance exams immediately after he arrived at Hiroshima, without undergoing the research student period. The exams took place about three weeks after he had arrived at Japan, andhad to be written in Japanese. I think it was 4 or 5 exams, but I don't remember well. Apparently, the reason why he was asked to do the entrance exam immediately was because the professor was going to retire in 2 or 3 years, and would not be able to supervise him fully if he had taken the extra year as a research student.
So, 8 months before the trip, the teacher gave my friend a list of all the Japanese undergraduate books that were necessary for his exam, and the guy, helped by his Japanese gf, studied like crazy. He almost had a breakdown, but he passed the exams, and from there it was mostly smooth sailing. He is now in Fukuoka after completing the master.
Another friend went to Tokyo University, to the education department: entrance exams must be done in Japanese, but only two foreign students can be admitted to the department each semester for the doctor course. Her Japanese was still not strong enough, and her research was in kind of a rut during the research student period. She asked for an extension of the research student period (6 months) and also an extra 6 months of scholarship. She had to ask for a recommendation letter from her Japanese supervisor, who agreed, although somewhat reluctantly. After 1 year and a half, she did the entrance exams and interview in Japanese, and passed.
Another friend applied for Architecture at Tokyo University. According to him, he easily spent two years as a research student, because apparently his teacher liked his previous work and was also interested in his current one. Probably, his teacher just told him to write his own recommendation letter in Japanese, and send it to him to check for errors. This also happened to me once (to extend my scholarship for the doctor course). At architecture, you can choose to do the exams in Japanese or English. There are 4 types of exams you can choose, 3 of them are a summary of the subjects you should have studied at undergraduate school in Japan, and the final one is to make a full architectural project in 4 hours. You only need to choose one of them. Every foreigner always chooses the 4-hour project, because as difficult as it is, it is no match for having to memorize 4 years of undergraduate japanese classes. The interview can also be done in English, and there are at least 10 classes conducted in English each semester. The architecture department also allows students to enter in April or October, which is a huge difference from other faculties at Tokyo University. If you choose to enroll in April, strangely you need to do the interview and exam 6 months before, and sometimes (depends on the department or whether you are in the master course instead of being a research student) a presentation of your work one month before April.
As you can see, the research student period is extremely elastic, depending on the goodwill (or not) of your teacher/supervisor. The dates for doing exams are completely different from faculty to faculty inside the same university, and from university to university. I cannot give any date, you have to confirm the correct dates by yourselves with the secretary of your chosen university.
When you first arrive at university, it is insane, but you might be asked (as I as) to fill a ton of paperwork by hand, which is exactly the same things you had to fill in the embassy application (you need to deliver the same forms at the university in 3 copies, all written by hand!!!!). YOU MUST bring copies of all your embassy application documents to Japan, because it will make your life easier, especially your educational background. You will need to fill those documents again when you apply for the master exam, and for the doctor course. NEVER lose them.
3 months before the end of your research period, you need to deliver the paperwork to apply for the master course exams. It is a pain in the ass, but be horribly meticulous when filling them and double-check EVERYTHING with a japanese friend.
You need to fill paperwork to extend your scholarship one year (or maybe 14 months) before it expires. MAKE SURE you do not miss the deadlines. When writing your expenses, MAKE SURE you come up with reasonable excuses and expenses to say that you are using up all the money given by the scholarship. This was recommended to me by the secretary, who said that if I don't do that, the government might diminish the scholarship for everyone.
There is an additional problem for people in countries where the Licentiate degree is given. Japanese people have no idea what a licentiate (licenciatura) degree is. Make sure that when translating the contents of your diploma into English, it is CLEARLY written that you have a Licentiate degree (add a explanatory note in Japanese saying what it is), or that you have a Bachelor. If not, you will get into serious trouble (I did).
I guess that covers everything. Good Luck to everyone!