hi arap!!! ^^
sorry i haven't monitor this thread lately, i'm quite busy packing my stuffs and prepare things though i have resign from my current job now.
i think menrui and ooilingfan have given a very good answer for your questions. i try my best to answer your question, hope it will be useful:
1. GPA sure is very important, i don't mean to let u down. but i'm sure that wouldn't matter if you had prepare an excellent research topics & proposal that could impress the judge. i don't know about other countries, but in indonesia submitting a research proposal is a must.
2. i have two recommendation letter, one is sealed, the other is not. i think you don't have to worry too much about it. sealed or not, you still have to make 4 copies on each of it, right?? oh ya, you have to use the form given by the embassy (official form), so i think two recommendation is enough.
3. well, as what ooilingfan have said just try to make it as clear as possible. if think the judges prefer a simple but well written one. just don't make it too long.
4. don't quit your job ^_^ you know that the waiting part for the final result is really killing us... i might space out thinking about the result everyday if i we're not busied by my job. i even think that one of us got insomnia while waiting for the result, right ooilingfan??
you've gotta work harder for your thesis from now, use your spare time. it doesn't mean that you dig your own grave when you being unemployed. some of my friends who received the scholarship even haven't graduated by the time of the application.
5. it's a really good thing that you already have a prof who is willing to be your prospective supervisor in Japan. i bet it would strengthen your chance to get the scholarship. he would be a great help to make perfection for your thesis
just give it a try ok!! i also failed on the interview round for this scholarship when i was applying for diploma degree, who knows that i would managed to get this for my master degree... ganbatte!!