I've gotten just about all the text flowed into iBooks Author. Thankfully, I was able to preserve most of the source formatting by using the "paste and retain formatting" feature. I just need to go through and double-check my indents and bullets/numbering (which were, sadly, not preserved).
More good news: I was able to copy and paste the diagram images from the text directly from InDesign to iBooks Author! I was afraid that I would have to manually convert each one to an image file or something.