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SVG will certainly be superior for the figures, and frankly I'd investigate using it for the equations as well, since setting them in xhtml/css is going to be a royal pain (ePub3 has embraced MATHML, but that's for the future).
Don't even bother touching calibre, it'll just introduce more work cleaning things up. Start from the ground-up in Sigil and keep the styles as simple and consistent as possible.
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