A bunch of notes, patched together through the use of an outline and copy and paste technology does not a quality paper make. There are two additional elements you must add: rewriting and thinking.
These two elements come together. You should expect to do SEVERAL rewrites--at least four. Every time you print out the paper and read over it, looking for ways to improve it, you will have ideas and questions which will improve the overall flow and sense of the paper.
What you are really seeking is coherence and clarity. Coherence means that the paper strikes the reader as a unified whole, all the parts of which are obviously necessary to make the point of the paper.
Clarity means simple, straightforward, easy to understand. Really good clarity means making hard to understand things obvious and clear to the reader.
Clarity and coherence can be achieved only by reading and editing a paper over and over again.
In addition, something extra may happen if you are really lucky. In the reading and rewriting, it will suddenly strike you that there is a MUCH better way to organize the paper and/or express your conclusion. When this happens it means you have REALLY learned your topic. You are a real expert and have added to mankind's knowledge.