Hi Arap, welcome to the thread.
I shall try my best to answer some of your questions.
First of all, I will not speculate on why you didn't get through last year, it could be 1001 possibilities. But i can comment on what's important to you.
1. GPA is important, critical or not, i'm not really sure. They do look at past results and your track record, but somehow I got the feeling they are more concerned of your future plans. I'm not sure whether they'll penalize you on GPA alone, but it's worth a try. Never try, never know, right?
2. How you submit the recommendation letter doesn't really matter. Last year we actually submitted the letter during the interview, which is not sealed (cause we need to make multiple copies of it, obviously we can't do it in a sealed envelope). As long as you have a good recommendation, it's fine.
3. Indeed, this is the most important part, you need to be as specific and as clearly as possible. However, I did badly in this part as well, hence during the 2nd submission (after passing the written test), i almost re-wrote the whole thing as per advised by the Embassy. Depends on how lenient your Embassy's committee is. They will only submit your application and documents to Tokyo in Sept/Oct so there's still time to amend if it's not well written.
4. Your employment status won't matter much. But I would advise you not to resign just to focus on applying for the scholarship. Reason no.1, the whole process takes approx. 1 year, and involves a lot of waiting time. If you have nothing else to do, it will be wasting your time, perhaps you can take up a full time japanese language course if you haven't learn it before. No.2, your scholarship is not secured yet at this point, in today's economy situation, having a job is better than nil. It will get worse, hence, JUST in case you don't get the scholarship, you still have a job. The scholarship is very competitive, you may need to try a few times. Don't risk your career. And you'll need some money when you're departing for Japan (about 2000USD), to buy your personal things and while waiting for your first stipend to be deposited. In fact, most of us only resigned after receiving confirmation or tentative confirmation of getting the scholarship (somewhere between Jan-Feb this year).
5. Getting a "verbal" consent from supervisor(s) is a very big plus!! If you read our posts, you'll see how much hardships we went through during the LoA application period.
Having a potential supervisor to advise you on your future project helps you a lot in drafting a very solid, concrete, specific, relevant and persuasive research proposal. Which will definitely help a lot during your application, especially during the interview stage, you will have a lot to discuss about and able to answer questions related to your research well.
I think that's all for now.
Most important thing now is to submit a complete application. Then pass the English written test. You may download past year questions from some of the websites (just google) and have a rough idea of how it looks like. You may need to score 80% and above on that paper to get an interview.
Good luck, and all the best ya.
p/s: there are Indonesians who got the scholarship this year. Athz being one of them but she might be busy with her work at the moment, haven't seen her posting replies lately.