Embassy scholarships are among the most competitive scholarships for coming to Japan because they offer a tuition wavier, point to point return airfare, and a living stipend (currently 144,000 JPY per month). On a GPA scale of 4 you probably need 3.5 minimum, and the top graduates in each country get these. (Many universities set a minimum GPA in lieu of taking the graduate school entrance exam - that is usually around 3.2 on a 4 point scale.)
I am sorry to say that with C's and D's your chances are not very good of getting an embassy scholarship.