I have a graduate student who wants to incorporate historical research into her graduate thesis. This is not my area of expertise, and I want to guide her correctly. I asked a couple of historians in my university for readings on conducting historical research, but they weren't helpful for whatever reason.
I know that historical research is not the same as research methods in the social sciences. I know about primary sources and secondary sources and how they build off each other. However, I do not pretend to know how a historian begins with a research question and then decides how to proceed in pursuit of that answer, how they decide where to begin, the different archives or databases that historians draw from, the primary errors committed in historical research, etc.
She won't officially start this component until the fall so I have time to do some reading and (hopefully) guide her in the right direction. I would be very thankful to anyone who can offer any suggestions.
It may help to know the "home" discipline of your program and the general topic (geographically and historically) of the research concerned. Revealing this may inspire more focused responses.
I have worked a great deal with archaeologists who have believed they are doing historical research when they consulted primary sources in anticipation of a dig. What they invariably missed is that a historian crafts research questions based on a combination of primary and secondary sources: current secondary sources can direct a historian in asking the questions that are pertinent for the current academic discussion. This is the part my archaeologists typically missed: by reviewing primary documents, they believed they "had done their historical research," when in fact, they only familiarized themselves with some historical documents - not with the pertinent interpretations and discussions that were unfolding at the time of the excavation. Not that all archaeologist are ignorant of the field of history (many are excellent).
I don't believe it is unique to the discipline of history when I say that a good part of research is knowing which scholars are to be trusted and consulted. Becoming a professional historian is knowing the bibliography and historiography - which historians should - and even must - be consulted and how the field has unfolded over time. These are both critical when beginning to shape one's research plan.
Knowing this is very specific, however, to time and place. Hence my initial suggestion. If your student is researching a topic that intersects with the English Civil War, the sources and current arguments in question will be very different from those associated with a topic that is related to the American Civil War. Both are civil wars, but the research strategies and questions and the available primary sources are world's apart!
Edit: also suggest your student use this subreddit as her research and challenges unfold. This is an excellent resource!
William Cronon, an acclaimed environmental historian at UW-Madison, has an excellent website that covers historical research methods (with many sub-pages) and includes references to many additional "standard" texts on research methodology. Some of the specifics are tailored to environmental history (e.g., "How to read a landscape"), but it's not a bad place to start in general. It is pitched at the undergraduate level, which is what many of your questions are reflective of (as opposed to the kinds of questions that would preoccupy a graduate student in history, which would involve historiography of one sort or another, a more advanced topic and a harder one to quickly learn).