The description of how you prepared to study the research problem, how you gathered the data, and the protocol for analyzing the data should be organized chronologically.
Remember that you are not writing a how-to guide about a particular method.
You should make the assumption that readers possess a basic understanding of how to investigate the research problem on their own and, therefore, you do not have to go into great detail about specific methodological procedures.
It is almost a given that you will encounter problems when collecting or generating your data, or, gaps will exist in existing data or archival materials.
Do not ignore these problems or pretend they did not occur. Don't avoid using a quantitative approach to analyzing your research problem just because you fear the idea of applying statistical designs and tests.