PLoS Computational Biology journal has published Ten Simple Rules for Getting Published. My favorite is number 7:
7. Start writing the paper the day you have the idea of what questions to pursue
Your papers should be concise, and impart as much information as possible in the least number of words. Maintain a good bibliographic database as you go, and read the papers in it.
I'm using CiteULike and have my own list with 110+ articles and books, most of which I have read. Still, I am struggling with the fact that I don't have a good way of capturing my thoughts. A getting-things-done-like system may help, but its focus is on managing tasks and things to do, rather than a bunch of poorly organized and (not yet) related thougths and ideas. Yes, I have a paper notebook, but it doesn't capture granularity of thought I'm after. I also leave many notes on papers I read and no good place to transfer them to. The system covered in How to make a complete map of every thought you think looks very promising:
You'll really have clear idea of what kinds of thought are going through your head. You'll really understand your ideas. And you'll also see connections that you were never consciously aware of. You'll see a structure and a pattern in your life. Your goals and psychology will become clearer to you. You'll be clearer too about what you don't understand. You'll be familiar with your mental terrain. Addictive clarity. Vast clarity. Exceptional clarity. Extraordinary clarity.
The book covers materials, general principles, intra-, extra-subject architecture, theory of notebooks (!) and has everything to get you started. You just need to have patience to do a lot of work to keep it going.
Here is another good article packed with useful and insightful tips for Ph.D. students
Your task now is to get to the central result as fast as possible. [...] There should be nothing before the main result that a reader does not need to know in order to understand the main result.
And another great advise on taking responsibility for your writing:
Much bad writing comes down to trying to avoid responsibility for what you're saying. That's why people resort to passive sentences, "it should be noted that", poor organization with literature first and your idea last, and so on. Take a deep breath, and take responsibility for what you're writing.
By the way, are you working on one of the most important problems in your field?