I am really unsure what you did and whether you began by exporting the PDF contents out as a Word XML (open the XML, should say in the header) by using Acrobat's Save As command.
You may have better success, depending upon the contents of the PDF, by first saving as a Word document out of Acrobat, doing any needed clean-up in Word, then placing that Word file into InDesign.
I converted a PPT to PDF and saved the PDF as XML. I then chose to "import
XML" within inDesign. So far, all I have is a panel of XML text, and am
not able to use the XML.
The XML saved out of Acrobat is not usable in ID. Not directly anyway and certainly not without extensive knowledge of writing and using XSLT file(s) to transform the XML into something usable. But this project really doesn't sound like a job for XML anyway.
Without seeing the PowerPoint file I wouldn't even know what to suggest other than just recreating it in ID. But, I would still investigate exporting the PDF to Word, cleaning up in Word and placing the Word file into ID.
I'd agree with MW Design. What InDesign needs to create good EPUB files are paragraph styles and character styles. You'll be more likely to do that by going PPT > Word which should retain most of the information. Then import the Word files and clean up and add any other styles in InDesign.