If anyone should be interested in this:
I got quite a lot of this working, and will continue working on it for a while.
Getting the math out of Word:
Mathtype does a pretty decent job of getting thing converted to latex.
It crashes a lot on OS X, especially if you forget to set the 'language' setting on export.
After exporting the content from Word, I still have to fix a few things , like two backslashes that should have been one.
Showing the math in Plone:
This is pretty straightforward when using mathjax.
If converting equations to images, it is difficult to 'keep the baseline",
Exporting to PDF.
This works quite well, both with pandoc and wkhtmltopdf, but some CSS is not working ( page-break-before is not working, while page-break-inside works). (Works on OS X Firefox, print to PDF)
Showing in epub.
I managed to shrink the JS to about 1,5 Mb.
The ebooks shows correctly in Calibre, iBooks (OS X) , Supreader (Android), Icecream Ebook Reader (Windows).
(but not in 'most others' FBReader etc).