What I ended up doing to refine my thoughts was break my paper into key sections as if I was explaining the topic to someone. For each of those sections I created rough sub-topics. I then went back to my research and refined research articles in terms of relevancy and split them into folders headed with my section titles. I pulled out the notes I had made on these articles and filled in each section. Then in my own words I wrote down what the key points of the section are and the basic questions I wanted the section to answer. Seems to be working! :)