Someone more knowledgeable than myself needs to comment on this issue as I don't really use calibre for conversions.
However, I don't think you're going to find this a simple solution. Or one that, with the right settings, can be handled just in calibre. I think you're going to have to strip out the text, use ebook creation software to take the text in and, with extra mark-up and effort, create a new ebook based on the old PDF material. This will be a complex project assuming you want to do it correctly rather than quickly. Particularly if this is meant for long term usage and data retention.
But I would keep the PDFs and the resulting ebook as well. Just in case.
