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Just got back to this...thanks everyone for the suggestions. I had assumed (duh) that because the IDs have to be unique across the documents, just the fragment identifier without the filename would work. Add the filenames and it's fine. The reason for fragment identifiers even when going to the top of the file was that the "top" isn't actually where I wanted to send users, it was one element down (just a matter of alignment).
Now I have a single XSLT2 program to generate all the files, plus a little script that extracts all the image filenames from figures, and copies them all into the epub directory, then zips everything up and creates the .epub file. Now comes the task of testing in all the common readers, and making something that Calibre can open and translate reliably to all the formats.
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