I'm about to put my third paper into 'percolate' status this week. I think the paper is pretty good, especially since I have a solution to the major problem presented in the comments.
It seems like a good time to share a few of the things I've figured out about academic writing. If you have more tips, please share...
1) Sticky-notes are your friend.
When I read books, articles or even my own drafts, I have three sizes of them handy.
I use the large ones to make more detailed arguments either extending what the author is arguing, noting how the passage may be useful in my paper or to write an objection to what I'm reading.
If I have a library book, I use a small sticky not in the book with a letter that corresponds to the big one... I'll often use the small ones to label sections of a book or paper so that I can get back there quickly when necessary.
The medium sized notes are useful for writing down sources I need to find, to make "to do"style notes about finding citations or checking on format issues etc.
All the medium and large notes go onto printer paper, NOT into the article or book -- this becomes a running and portable set of notes I can then stick into drafts of the paper I'm writing, arrange in other ways or generally move around. If they are in the paper or book, they are stuck.
Also, I use stickies to make notes that occur to me about future projects. They go on another piece of paper for later reference.
2) Sometimes starting over is a good idea.
Take the weakest section and write a complete replacement. Start a new document and write how you think the section should look. When you are happy with it, insert it into your paper. Your experience with the material will often turn your weakest section into the strongest.
3) Time is your friend.
When you are working on a paper, decide on stages at which it needs to "percolate". Time will give you fresh eyes about the paper and let you sort out the knotty problems associated with all good papers. Of course, this requires some advance planning and time management :).
Before you put something on "percolate", gather all the references you cited in the paper as well as all the sources you think you may want to include. This will prevent you from having to re-do research later -- and it may save you a lot of time.... Trust me, I've skipped this step -- don't do it!
Also, before you put a paper away, make a "to do" list. Sketch out the problems you see with the paper when you put it away. You should remind yourself to check for your bad writing habits.
Then, don't look at it for at least two weeks, maybe even a month.... really, don't do it. Start another paper, clean your closets or catch up on grading -- just don't work on that paper!
I hope those things work for you --