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Like others said as well, forget about it. Not only is PDF one of the worst of formats to start from that will require a lot of manual work, it also seems that the books you are describing are probably better off as PDF. Tables are a pain in ePUB, especially due to the reflowing and font size changing characteristics. You could consider a fixed-format ePUB, but that opens up some whole different can of worms.
In short, don't do it. Also, why is this actually needed? What can't you do with the PDF what you can do in ePUB? These kind of books will not benefit from a reader and will probably need a tablet of computer anyway and reading PDF is fine on that. If the problem is searching, then the PDF was created in a wrong way and OCR is your only option. Then you can always use FineReader to OCR the PDF and save it as a PDF but now with the ability to search in the text.
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