From what I gather the research proposal is similar to a statement of purpose, a document which justifies to the Mombusho why your studies/research is worth funding. It also states what specific areas of research you plan on exploring. The study plan I think is an essay which tells the Mombusho why you want to study abroad and what areas of self-study you will be involved in for the pursuit of your studies/research (study objectives).
You should clarify this with others over at the following website which is targeted specifically for those who are on study with Mombugakusho.
monbusho.org
Other information may be found here:
studyjapan.go.jp/en/toj/toj0302e.html
Here's other tips or writing a research proposal (geared more towards scientific research but good information in general):
sciencecareers.sciencemag.org/career_development/previous_issues/articles/1820/writing_a_research_plan
Hope this helps.