I can't answer all of your questions but I will answer what I can.
1. I recommend going the way of "research student" first. The benefit here is that you can arrive in Japan and already be on scholarship while you prepare for and take your entrance exam, and if needed you have up to four chances to take the entrance exam in the two years you are allocated as a research student.
If you want to go directly into the master's or PhD program, you are required to travel all the way to Japan to take (and must pass) the entrance exam in order to be finally granted acceptance to the school, and thus ultimately the scholarship as well.
2. can't help you on that one, sorry...
3. The way it works is, if the consulate recommends you as a preliminary candidate, you must then make your best effort to obtain a letter of acceptance from your proposed place of study. At this point you are not yet necessarily granted the scholarship, the selection process in Tokyo is still to follow.
The application guidelines say that the Monbusho may make an effort to find placement for you in the event that you are unable to gain acceptance or if for some reason later on in the process the university is unable to accommodate you, but it would make a lot of sense if they'd prefer those who have gotten acceptance somewhere. My impression is that many of the successful students I've run across have had professors who were receptive/interested to have them somehow or other. This doesn't have to be 100% true all the time though.
4. You don't necessarily need to list alternative placement choices. I only listed one. However, in my case my proposed study was quite specific to the department/professor I chose, and before actually submitting the application, I had been in contact with the professor and gained his support to some degree. If you are not so sure that the advisor you propose will accept you, it may be a good idea to get in touch with some alternatives.
5. The interview was pretty quick for me, they just asked me briefly about my proposed research, my previous experience with Japan, what did I know about the city/university I had chosen, and a couple simple questions in Japanese. It ended in like 15 minutes but felt like five, and going out I didn't feel I got enough in depth to fully demonstrate my qualifications or interest in this endeavor, but it worked out OK anyway.
The Japanese test is basically just to gauge your ability. You will also have to take an English test, and the requirement to get the consulate recommendation is that you pass one or the other-- just to demonstrate that you are proficient in a language in which you can communicate with your advisor. The Japanese test is also used to place you in a preparatory language program if necessary. In the three parts of the test, I whizzed through the easy one, had not too much trouble with the medium one (could easily pick out the meanings and main ideas of words that I didn't even know, to answer the questions) and then got *nothing* on the last and hardest one. The university still decided not to place me in the 6-month intensive program based on that.. so I'd say if you can do JLPT 2, the Japanese test will be no issue at all for you.
Since your proposed field is a social science kind of thing, and hence more likely to be language-inolved, they might expect Japanese language ability from you, but like I said, being at JLPT 2 level is plenty.
Hope that helps!
