Did you make notes on the journals you read and then piece them together later, or did you lay out the structure of a document from the start and fill it up with random paragraphs and references as you went on?

I didn't anticipate the journal filing system issue with a PhD! Cross-referenced to notes and databases. I hope my chosen system is good for the next three years!

If you start writing up at the same time as reading, there will be no need for a filing system. For example, you read a paper for your lit review, and write three sentences about it into the lit review draft word document. Plus, you'll always have a draft version of Literature Review, Methods, Analysis, .... at your hand. will save you a lot of time in the end.

Wise words. I didn't do that! I have a mountain of literature and very few notes except on one part which is fairly complete.

Sometimes it works backwards too. You know what you want to say and search for a suitable ref to pop in.

You could try this to get started:
Huge sheets of flipchart paper.
One sheet per 'theme/idea/hypothesis/chapter'.
Brainstorm.
One absolutely focussed day per item.
In five days you will five 'topics' or 'chapter'
This may form some structure for your project.

It worked for me.