File structure, file structure, file structure. It's the same with organizing a story as it is organizing a building design. If you can sort out your files in a way that flows logically, then you won't spend time thinking about where to put things or where to find them. If something doesn't exist in the place you know it only could be, then it isn't there.
For instance, the top level might be Art and Story, just split things in half right there. Art might them become Characters, Landscapes, Buildings, Pages, etc. Within each you go to Reference Images, Rough Sketches, Line Art, Finished Drawings, etc. And you can see how this goes. Bonus points if whatever format you're using allows you to couple notes with an individual file. If not you can safe a text file with the same name as the file with your notes, so they get sorted. Ext to each other.
Additionally, if dates are important, date the damn thing! Preferably with the date up front such that the files get sorted chronologically when sorting by name.
As far as keeping the story together itself, it's very much the same thing on the file side. You seem to be getting an idea together already. But know you have got to have a skeleton. Descending bullet points, a legend, a little blurb about what happens as you go along, whatever works for you. The important thing is that you are able to swap things around in a timeline sense without having to refigure out your formatting. Once an entry is made into your skeleton, it should function as an independent Lego that you can move around.