I tend to go for notes chapter-by-chapter. Among other things, it takes long enough to read a chapter that I get to the point where I can remember any particular idea with ease but the flow of concepts has mostly been lost and all of the pieces have been shunted into long-term memory. If I can mostly reconstruct the chapter, great, if not, I go back and figure out what was where and why it was there. (It might be worthwhile to always go back and see what you missed / got wrong, but that would probably get close to doubling the necessary reading time.)
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.