Indesign to ePub formatting issues (first ever attempt)

Okay, first the good news: you were correct to select reflowable as your EPUB model. The number one mistake most newcomers make is that fixed pages are "easier" or "more natural" or some such, and they're wrong; e-books should be liquid, reflowable text.

Unfortunately, your second choice, overall, was to make the common assumption that an EPUB can be created by just exporting a print layout to that format. It can't. Unlike PDF, which was designed specifically to replicate print pages in digital form, EPUB is representative of the proper e-book model, which is quite different from print form. It demands many changes from a purely-print layout file.

You might find these two essays useful in getting a quick grasp of the differences, and format/layout needs for EPUB in InDesign:

• http://www.nitrosyncretic.com/DPR/dpr_indesign_epub_basics.php
• http://www.nitrosyncretic.com/DPR/dpr_indesign_epub_image_mgmt.php

But let's go through a quick list of the obvious problems with your ID layout as it needs to be prepared for EPUB export.

• First, all elements in an EPUB export need to be contained in one text flow, and any "loose" elements like images or TOC frames need to be anchored to a specific spot within that flow. Multiple text flows will have unpredictable results in the outcome, and any unanchored elements will simply fall to the end of the document, as you've discovered. That, overall, is the single most important element to keep in mind, and it can be a high hurdle, since many print projects are just stuff stuck all over the pages, without regard for the underlying structure. Pages print like pages, but digital export looks only at the technical structure of the document... and that can be wildly different if you haven't followed this basic rule.
• You shouldn't really include/spec/embed fonts in an EPUB. Let the end reader, especially Kindle Reader, manage fonts and text as it prefers, as it will, anyway — so you can fight it and get lousy results, or respect the different medium and get great ones.
• An inline TOC isn't really needed in an ebook.  What you want is a well-defined TOC structure with no page numbers or assigned formatting, which can be deeper (going to second and third level heads, for example) that is called up by the reader (the app or device) and not presented as pages in the document.
• A cover in an EPUB is not your complete print wrap-around layout. It's just the front cover, in JPEG or PNG format, about 1000x1500 or so (proportional to the print cover, if you like), added in the export stage by specifying that file. It is embedded in the correct location and structure in the EPUB and used by Kindle Previewer, but know that it's discarded in Kindle publishing, with the cover you upload to KDP used instead. But there should be no "cover" anywhere in the InDesign source file itself.
• As for graphics, see above; they need to be placed in the single text flow and anchored to the end of the paragraph they're supposed to follow. There are many, many aspects of formatting them to appear in the e-book as desired, but for now, make them margin width, centered, anchored to the prior paragraph, and export using the Fixed CSS option as a first pass.

Absorb and apply all that, and come on back with your next questions. 🙂

If it's not clear, you will want to work with a separate copy of your book file for EPUB — you will mess up the print-ready version a ton making it suitable for EPUB export. (It is quite possible to have/use one ID source file for both, but that's an advanced technique.. Best to use two separate ones, although that means you will have to carefully update each in sync if you make changes.)