What challenges do you anticipate and how do you expect to
overcome those challenges?

The topic doesn't go with the research so go more along the lines of the actual topic given. Im not sure about in the actual paper about the aim of the research, the patients, the data and methodology. The patients cannot be made up and whatever you put in the paper It is assumed I will have done, so nothing needs to be said about me conducting research. Furthermore, no “human subjects” according to the IRB should be included.
Now I want the Proposal Progress Report to be second document, the Written Research Proposal the third document and so on as in the instructions listed previously.
I will also need footnotes added to the Written Research Proposal.

The Progress Proposal Report
May be up to 5 pages in length (including title page and bibliography page). The narrative should answer these questions
What is status of the project? What has been accomplished thus far?
What topic do you plan to study, and what do you hope to learn through your research?
What are your tentative plans for conducting your research?
What challenges do you anticipate and how do you expect to
overcome those challenges?
How have you begun to consider the following: Who, what, when,
where, how, and why?