It'll only take you half an hour to go through the entire manuscript, one error at a time. I know it seems like a lot, but once you get going, you'll have less and less to correct as the distance between corrections gets longer and longer.
Yes, I'd second that. I don't use Word, but Pages, but I assume they work in similar ways. I would NEVER write my novel in one long, ponderous document. All my chapters are held in separate documents. I made a template at the start, so they're all in the same format. I've divided them among 3 folders (Beginning, Middle and End) and stored these folders inside a main folder marked with the name of the novel, which also contains Research, Story Ideas and Story Timeline folders. This makes it very easy to chop and change between chapters, and makes it very easy to do backups of anything I've just changed. I don't have to back up the entire book every time I change a couple of lines in Chapter 23. If I were you, I'd copy and paste each chapter into a separate document. Label each one with the name/number of the chapter, and maybe include a footer with separate page number and chapter name, so you can tell instantly what you've got. You can also duplicate and date each chapter with the date you alter it, so you won't get mixed up and possibly ditch the wrong version. (And save past versions in a separate folder, in case you want to recapture any older bits.) LEAVE YOUR CHAPTERS IN THIS FORMAT until you're actually ready to merge and send the whole novel out for publishing. This would solve your spellchecking problems immediately, and make your edits and backups easier to manage as well.
