At this point I'm afraid I'm going to bail on the Calibre-conversion approach.
Even if I write the JS necessary for it, it will be painful to achieve the level and granularity of control over the outcome that I believe I need. And your previous comments that "All available variables are documented" leaves me uneasy about achieving the level of quality and control I can exert even via JS. The converter goes a long way towards providing an acceptable finished result, but not quite far enough to have confidence in extra effort being rewarded with the desired results and absent quality compromises I don't want to make. Another sign of this is the lack of other forum members leaping into the discussion with testimonials of success and any suggestions of how to proceed. So while I regard the attempt as a noble effort, I don't want to devote any more time and effort to it. I think the converter is a great tool for producing PDFs for certain purposes, but not for fully polished results for publishing. This isn't a knock on what Calibre does in this respect -- just a recognition of limitations and ease of use. So with reluctance I've decided to move my Epub version into Word and produce the PDF from that environment -- navigating the minefield that is Word with care, but with a feeling of better control.
It's taken me about five minutes to have Sigil merge all the XHTML files, suck that single file into (yikes!) Internet Explorer, and save the result as a .docx. It looks surprisingly good and without obvious distortions or errors (though who knows what trash Word has created under the covers). Now it's a matter of creating the appropriate styles and templates, but even under the worst case that shouldn't take me more than a week and I'll be able to fine-tune the result. A major added advantage is that I'll be able to generate and edit an index within that environment -- which, even with a successful Epub conversion would be challenging and painful (or expensive).
I do appreciate your rapid responses to questions and all your efforts to help. But at this point I think discretion is the better part of valor.
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