Missing random photos in epub export

I am converting a print book to an ePub. I built the layout in a word processing document in Pages, using inline images, text styles and flush, right and left images. I then exported the file to the ePub format. It is a large book with 400,000 words and 300 images.
The final product looked great until I started noticing that there were photos missing throughout the document - about 115 out of the 300. There is no pattern to which are missing - i.e. 40 in row are fine and then 3 in row are missing. I used 3 different alignment settings for the inline images and some of each all appear fine. The images are all dropped in using paste from an InDesign file that contains a photo with its caption so as to keep the caption with the image. The dropped image is a pdf that the epub exporter converts to a PNG file. In the xhtml files inside the epub, there is no reference at all to the missing images - the image numbers completely skip them and the code just has a space where the image code should appear.
I was hoping to be able to get close with Pages to ePub and then make minor tweaks to the finished product. I didn't expect to have to hand convert 115 images into PNGs, hand code them into their exact location, code the reference into the OPF file and then assemble it all again. Seems to strongly point to an "undocumented feature" that is ignoring random images.
Any help or ideas would be greatly appreciated. (I've got about 40 hours into converting this book so far and it looks like it is going to add about 20 more to manually fix all these problems and manually check the output.)
Thanks,
Wade

I was not able to solve this problem using Pages. I took the problematic ePub I exported from Pages and used it as a starting point. I did a bunch of research on the ePub format and figured out how to solve the problem manually. (Make sure you use the latest version of the iTunesConnect_PublisherUserGuide.pdf as it gives a host of great information and things you have to do for it to work.)
I ended up getting technical and cracking open the ePub file into its component parts - META-INF, mimetype, OPS - by changing the ePub extension to zip and then using Stuffit Archive manager to export the contents. (In a ton of research I found all about the structure of the ePub files and that it is basically a ZIP file with some special qualities.)
Inside the OPS folder is basically a web folder - with an xhtml page for each chapter, css files, image files and a couple of ePub specific files. I used Dreamweaver to edit the problem chapters and placed the missing images. Also, I converted all of the "dropped images" I brought in from InDesign to PNG files (they contained the image with its caption so that it stayed formatted and in place with the picture). This served to make the overall size of the ePub smaller, as we were bumping up against the iTunes size limit.
The item that has to be done or this won't work is to correctly modify the "epb.opf" file that is in the OPS folder. When you open it, you will see the pattern of how every image placed in Pages is listed/referenced in this file. From there, I had to add the appropriate reference to every image I had added and make sure that there were no extra images referenced. The ePub will not validate without this step. (Another tool I used was ePubChecker - it will check for this and many other things that will cause your iTunes validation to fail. Invaluable.)
Once I made all the modifications, I used ePub Zip 1.0.2 to correctly ZIP all the files and convert it to a validatable ePub file. I couldn't create the right kind of ePub file - with all the meta data set correctly - using Stuffit. (Had something to do with how something wrote out from Stuffit). ePub Zip did it perfectly.
It has been a while since I did all this, and it was an all-nighter, so I may not have listed all the details here. If I have not explained something clearly or left something out, please let me know.
Hope this helps. It wasn't much fun, but it was really awesome when it finally succeeded in uploading and validating on iTunesConnect. Then we had to wait at least a year for it to appear in the store. It was a little over two weeks, but it seemed close to a year. Good luck with your book!

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