I've also taken the larger crit notes and put them in one master critique file. Next (harder) step, as the kids allow, is to go through the larger notes (like, "why doesn't Captain Raj believe Gaurav? address!"), which may require re-writing entire paragraphs or longer sections, or generating new material, or cutting things (although likely not much of the latter, because I tend to write overly-lean to begin with).
If this were a short story, I'd then follow with a final step of retyping the whole damn thing, because I find that helps me keep the voice coherent and clean. For 40,000 words, with kids at home and a cold, I'm not sure if that last step will happen -- hopefully, if my hands allow and if Kev can find time to keep them for a while (he has his own deadlines), I can do that for at least part of the book. And that's the writing news from Oak Park...