I've been converting a 300 page book from Word for Mac with a lot of boxes, charts, and graphics into ePub. I think you'll have to place each image into one program, Pages, Word, Word for Mac, InDesign, PhotoShop, or whatever. Then Calibre (free) will convert it to an ePub doc for Kindle, and iBooks. Pages from Apple converts to ePub. Create a Kindle account (free), upload it and use Kindle's previewer to see what it looks like, as Kindle is one of the main publishers. Or do so with iBooks, which I'm getting to next.
For the Table of Contents for Word, try using hyperlink with bookmarks to jump to each chapter. The usual Headings method that is shown for Word works, but the result is clunky looking, which then needs HTML work to spruce up.
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