Sometimes when you have loads of files, it can be hard to organize on the computer.
Maybe you should make yourself an index to it. If you did it in Excel, you could have a column for the subject heading, a couple of columns for other possible topics or subtopics it could fall under, and then a short description of the contents, and the file name.
Once you have them all in the file, you can sort by your headings and subheadings, make adjustments, sort, and so on. Once you've got it organized into groups you could start deciding what order to present the material in.
I'd probably put the files related to each chapter in separate folders and then start merging and editing them.