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Multiple books merged in a single PDF file? What were they thinking??? It's difficult enough converting a single column, simple PDF (and sometimes with unexpected results), let alone a complex document with variable widths for pages. I would probably export the PDF as a bunch of images. The e-reader should have no problem displaying those. And if searching and highlighting is important, you can apply "good enough" OCR with ABBYY FineReader – and maybe save as it a PDF with your reader's screen dimensions because the Mobi format probably isn't very good at positional OCR (text under images).
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