I didn't invent this. The amazing Rachael Cayley @explorestyle did: http://explorationsofstyle.com/2011/02/09/reverse-outlines/

The first 3 months of a PhD is too early. After that--it's hard to start writing too early.

Now I do this with a pen and paper and a list.
Patrick Dunlevy recommends the index card view of PowerPoint.
Post its would be great.
If you're generally good at writing topic sentences for your paragraphs you could just highlight them.

Proportion: do you have the right amount of each section? Rough guide, 10%+ intro, 10% context, 10%- conclusion.

Logical sequence: do you start with a first principle and explain it, step by step, so anyone can follow you? Remember with original research no one else has ever been this way before.

Coherence: Does it hang together? Does each part follow on, and flow forward? If not, have you given your reader a bridge (a simple "However" or more).

Rhythm: The best academic writing has something else about it. Sometimes it has narrative tension. Sometimes it has elegant cadences. Sometimes it is snappy and crystal clear. It has style, it has clarity and grace. (Read Helen Sword, or William Colomb for more).

Reverse outlines are a map of the territory, they follow the contours of your writing. They allow your write to be organic (which tends to be better for coherence, proportion and rhythm), and to allow your texts to be structured as academic prose (not super lists), which tends to be better for logical sequence.