In today's work session, I'll make a new version of the file and accept all my changes. (I work in Microsoft Word with the 'track changes' feature turned on, specifically so I can backtrack as needed.) I'll also combine the two separate .docx files that are part I and part II of the book into a single .docx, this to facilitate search-and-replace operations as well as moving back and forth around the body of the book. These are purely technical issues that I need to address before getting serious about the second revision pass.
One of the purposes of that close line read is to load the book back into my head. This way, when I have a note on page 532 that says something like, "Did Mist know this earlier?", I have a pretty good notion of where the earlier scenes are that Mist might (or might not) have been in on that particular revelation. This sense of having the shape and details of the book in my head, within my span of control, is critical to the second and later passes. (For more on "span of control", see here and here.)
The second revision pass will be to address scene level and structural issues, which is what the majority of the embedded comments are concerned with. My agent made a suggestion that will greatly improve the dramatic tension of the book, but requires serious adjustment to a major plot thread and a fair number of minor clean-ups elsewhere. This will probably not take me too many elapsed work days, as in revisions I am a very conservative tweaker rather than a tear-down-and-rebuild kind of writer. I trust Fred, my writing mind, and I strive not to damage or blunt the voice that is always strongest in my first drafts and only ever minimized by too much revision or polishing.
After that, I'll go back through again, most likely focusing on character issues in the third revision pass. I'll also somewhere in here decide if a fourth revision pass is necessary or not.
Note that none of these revision passes are surgically clean. Even though the second pass is about scene and structure, I'll be noodling character issues while I'm in there. And vice-versa for the third pass. The process is rather more organic than I'm making it sound here. But in a high level sense, this description is accurate.
I am also pleased to report that I seem to be somewhat ahead of my own production schedule. This monster, which will ring in at about 135,000 to 140,000 words for Calamity of So Long a Life, may be in to my agent a week or two early. I'll spend March working on short fiction and letting my brain settle, then in April it's on to volume two, Their Currents Turn Awry, of which the first 70,000 words already exist in draft.
I love this stuff.