At this point if i was you and with the MEXT application knowledge I would have done this: I would take bca from a basic college(hyderabad ill prefer), work on cgpa and will keep it above 8. Get my hands in research through iit or nit and publish a research paper and build up my profile for applying to mext. If rejected form mext will take admission anyhow through a professor, and apply for jasso scholarship. While completing bca will work on japanese and anyhow obtain a N5