Ok this is really weird , well i did send a lot of emails to them but they never replied , and I was a bit confused when they sent me the application in Japanese.
Usually it is the Embassy's responsibility or whoever gave you the MEXT scholarship to send your designated university the letters of recommendation that you already submitted when you applied to the Embassy as you are not supposed to see them being sealed and all .
(This is also what happened when I applied to the other University). However I am not sure of your country's policy considering this matter, I say consult your cultural attache or the person who is responsible of the scholarships from your Embassy.
To tell you the truth in the application that they sent , they didn't list any recommendation letters as a requirement, although am pretty sure that they are needed. I guess they didn't get the idea of me being a MEXT student.
In their application they ask you some general questions like : personal info Education background, sample work , study plan and proposal , ... (I shall send you more details when i recheck it at home ).
In your case, I suggest you send them the items they requested. It is always better to send them your resume or any application in Japanese, however, if you can't you can simply state your level, but mention that you will be improving your Japanese level as part of the scholarship requirements.
I am not sure if this is good advice , but this is what I intended to do with my application: fill it out in Japanese (with the help of my Japanese friend , as am still considered a beginner in Jap ) and work on my Japanese later.
In our country you don't have to know Japanese to get the MEXT scholarship (it is a bonus though) as they give you intensive language courses when you go there.
Am pretty sure the university knows that as they acknowledge the MEXT scholarship as part of their admission.
As for the stamped papers, I believe you should send them the ones you sent to the Embassy, In my case, the Embassy sent me back one copy of the stamped applications that I submitted when I applied to the MEXT scholarship ,except for the recommendation letters. when I asked the Embassy for them , they told me it's their responsibility to send them to the university. So try to ask your Embassy for another copy of the stamped papers before going through all the trouble of filling them out.
I hope I helped a bit , I shall send you any more info I find considering this university or the application . Good luck !