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Just a shot in the dark. Everything has to match and the HTML spaces could cause a problem. You might try changing the name of the file so it is more like the id with underlines instead of spaces. Then use search and replace to find all the old names and change them to the new name. Also case counts, so if it does match for case it will fail as well.
If you get desperate, you can save out of Word as filtered HTML and take it into Sigil to fix it up. There will be a large amount of junk which should be gotten rid of, but you might be able to create something useable in the limited time you have. If you make your chapter names headings (h1, h2...), then you can use Sigil's generate TOC to generate an epub index. Note this is not the same as for Kindle. But I understand you can take it into Calibre to generate a valid Kindle file.
After you get done with all this, your next opus can be "How to Save your Sanity while creating E Books." (grin)
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