Based on the great comments I have received I decided to take a stab at answering my own question.
A large part of the problem I have is that I have been procrastinating as @erikric suggested. However, I think that just solving it using brute force time management techniques duck the real issue here - that I feel uncertain as to what to do when I'm done free-writing. Thus, I outlined a process that could potentially describe how to cycle between the different stages of writing.
Graphical representation of writing process (can someone insert this picture in the post?)
Generative Writing. This is focused free-writing, or generative writing. Essentially a stream-of-consciousness focused on the particular topic or question that I am working on for the moment. Often this is based on weaknesses in my arguments that has been pointed out by those who reviewed the last draft.
Read & Develop. This is a first review of my free-writing. It is not an editing stage but rather a way of a) getting an overview of what I have written, and b) an attempt to squeeze some further thoughts and arguments out of my mind before I move on to editing.
Outlining. Here I start to outline the paper chapter by chapter, paragraph by paragraph. This means that I need to describe the major points of each section (i.e. chapter or paragraph) so that I get a clear view of what each section accomplishes and how it fits into the paper as a whole.
Rewrite/Reconstruct. After I have created the outline I can start to rewrite or reconstruct each section. I use the term rewriting for a section whose basic integrity or structure can be retained with changes only made to the way the section accomplishes its goals. The term reconstruction is used for paragraphs that, according to the new outline, needs to be rewritten from scratch, because the basic logic of the paragraph as it stood before the outlining process does not make sense any longer. While particular thoughts or sentences will be retained, it is easier to write it from scratch.
Gather feedback. I will send it to my advisor and/or research group for feedback. The whole process continues until the paper has been published.
Upon reflection, I realize that I have often not done the outlining stage (meaning, I have skipped it completely). Also, I have often attempted to rewrite when I should have been reconstructing. It makes sense that if someone just tries to make minor changes within a structure that no longer works, not much good will be achieved. All that will happen is that I will have this feeling in my stomach that something is wrong, but not knowing how to deal with it.