Questions to Comments on Exploratory Essay

The best/most helpful comment that I received on my paper was the second comment. The comment says that I need to spend less time summarizing each work and more time analyzing how that work relates to my overall theme. My themes are how and why some students react to learning differently than others and why some students overcome their deficits while others can't. In the comment, Megan says that I need to spend more time explaining why. Why do some students react differently to education than others? Why do some students overcome deficits and others don't? She says to make sure to back up the whys with evidence FROM THE AUTHOR.
The least helpful comment that I received was the comment that says that I need to stick to the author's arguments and leave mine out of the paper. This was the sixth comment. I am confused about what should be in my paper. In the fifth comment, Megan says that she is interested in my ideas and analysis, but in the sixth comment says that I need to stick to the author's claims. This confuses me about what part of my input I should put in the paper. I think that if I had this confusion cleared up, it might make it easier for me to write a better paper.
Some questions that I have from Megan's comments:
-In MLA, are you supposed to do in-line citations or citations at the end of the page or at the end of the paper?
-When I have questions that I am left with from the readings, do I just state the questions in my paper or do I state them and then try to find the answers in the paper or with outside sources?
My plans for revision include general editing. I plan to fix some of my grammar issues. I am going to cut down on the summary of each reading and spend more time analyzing the reading. I am going to spend more time on the why of my themes and how my each reading relates to my overall themes. A big thing that I want to fix are my citations. I need to make them more MLA friendly.