@MayJay
I don't want your question to be ignored, but the thing is usually the embassy will not give reasons for why they did or didn't select a candidate, so most people won't know what their weak points were.
Whether your particular grades and experience are enough depends not only on which embassy you apply to, but also who else happens to apply that year. The field of candidates might be particularly strong or weak this year at your embassy.
If you really want to study in Japan, I think you should try regardless. If you already have experience and a couple of research papers, and on top of that speak a decent amount of Japanese, it seems like you have as good a chance as anyone.