I feel like my first draft is a hunk of word matter without much organization. What have you done in the past to whip a draft into something palatable?
My writing 'unit' is the scene. Scrivener allows me to have a separate file for each 'scene', to view and read and export and print them individually or in groups, to drag them around and re-order them and put them in folders or subfolders, to take notes about them (for example, notes on what I have to fix now that I've re-ordered them) and to tie a variety of other data (keywords, meta-data fields, etc.) to them. I realize that's just a tool, not a method. If I had a not-much-organized draft, my first step would be to cut it up into scenes, to allow me to use that tool most effectively.
I second ChickenFreak's suggestion (Would that be "Mr. Freak"?), but I would also add that I would try to identify novel structure I used (15 beats, Hero's Journey, traditional 3 Act, etc.) and try to identify what parts go where in that model. If I didn't USE a structure, I'd try to figure it out as a 3 Act structure, but that's me.