Without going back to an outline, you could do the following:
* Print your draft on paper.
* Take some fluoresecent colored pens and mark all the words that are specific to your paper. Not words like "the" and "research", but words like "unification algorithm" or "eukaryotic cell". Use different colors for different topics in your paper.
* If you see the same words/colors in many remote places, move those sentences closer together (you're obviously back behind your computer now ;-). Ideally, each section talks about a single topic, so it should have more or less only 1 color. Since your paper was a "sea of words" to begin with, you lose nothing by moving things around. Never mind the "flow" for now: just the topics.
* Now that the topics are "sealed" into sections, remove all duplicate sentences. 487
Keep only the ones that give new information.
* Order the sentences so that new terminology/ideas are introduced in a logical order, i.e. new words/concepts are defined before they're used.
* From each group of sentences, make a temporary title and put it in front of the group. It may not make it as a title into the final paper, but it brings an outline back into the paper for yourself.
* Now, and only now, start looking at the grammar and the flow. Turn each group of sentences into a few paragraphs right there underneath their temporary title. Make sure that each group expresses exactly the idea in their temporary title.
* For better "flow", start larger sections with a summary of what you explained in the previous section, and then show the connection to the new section. You can quickly see what you explained in the previous section by going over their temporary titles.
* At the end, take all your temporary titles and turn them into a summary. You can use this as the introduction, the conclusion of the paper, or even both if you rewrite it slightly.
* Then remove most of the temporary titles, keeping only the "big" ones to structure the paper for your readers.
Regardless of which technique(s) you use from the many excellent answers, let us all know how it worked out for you! Good luck. 487