I think you should get a rough draft written as soon as you possibly can do so. In many ways, this is the hardest part of the process. The way to move on this is in chunks:
- Write the Introduction, Background, Methods, and References sections first, and add to them and edit them as you go along. These sections are not going to change too much.
- Write the Abstract last, obviously, after you have written the Results and Discussion sections. However, you can write the skeleton part of the Abstract since it usually has a little bit of introductory text and background.
- Plan on using the Statistical Analysis Plan layout to organize the Results section of your manuscript.
- Plan on writing the Discussion section in parallel to the Results.
Note: Until you have the Rough Draft done, I recommend not showing it to anyone on your committe including your advisor!
The reason for this is that you will simply get sidetracked by your committee members brainstorming, knee-jerk criticism, and helpful ideas. It is all too easy to get caught up in an endless cycle of changing the statistical analyses and results in order to try to hit illusory targets.