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It's a sloppy implementation on my part but the HTML and javascript are all in the same HTML page and it works on my apple devices in iBooks when I create the EPUB.
I'm going to say the files are relative to the links to the javascript.
The div webvtt and data-audio and data-VTT I mentioned above is the only reference in the entire EPUB to those files. The Javacript looks for those declarations and runs perfectly.
If I'm doing something wrong or could do it better then I'm definitely here for that as right now I'm just creating a link to those data files within Sigil for each ebook then pasting them into the DIV section as shown in the original post and then deleting how I'm getting the link into the document hence why I'm asking if there's a better or easier way.
I'm sorry if that doesn't answer the question well enough.
By the way I do like the suggestion to keep an EPUB as kind of like a template and I've started doing that, thank you.
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