Hi oula!
I think that, as have been said before, many things depend on the embassy procedures and how they carry out the applicatin process. For us, at some point they hinted at the embassy that they had really looked closely at our transcrips as that reassures them we are capable of very good results and will not let them down academically wise. That said, many here have said that in their cases it didn't matter much.
Also I agree the reasearch proposal and clarity of why studying in Japan is the how they make the final decision. Least important should be, and is, the major you have. As long you can prove you have a good study plan and are focused on what you want to do.
As for the spouse question, it is not my case but, for example two marriend couples from my country, they both hope to get the scholarship eventually, but as places are limited and it is a very sought after scholarship they decided to keep their chances high by not competing against each other. The idea is either wait for next year for the other to apply, or travel as a dependant but use the contacts of the spouse who got the scholarship to gain a University Nomination. So far no one at the embassy has told them it is not possible for them to both recieve the scholarship, whether by this method or just applying at the same time. In any case asking directly your embassy would be better.
I too would strongly recommend not tricking your embassy or MEXT, such things always end for the worst; and a great opportunity may go down the drain because of a stupid decision like lying on the aplication form. ( Sorry, I didn't see your last post, so it was a hipotetical question after all! I'll leave this bit in just in case anyone else get funny ideas)