I don't know of a better tool. Yes, it has severe limitations, but that's because you're working against the grain. PDF was meant as an output format, it wasn't meant to be an input format for converting to others.
But I'm confused by "Using Calibre to me means starting from scratch with CSS and many, many other things." That seems to suggest that you had created a CSS file to begin with. Surely if you have access to the source files for the document, you're much better off using those to create your ePub, and not using PDF as an intermediary.
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