First step in converting PDFs, is to get a decent PDF... what you describe is a PDF which has the original scan image interleaved with badly done OCR... whilst this allows a clear page to read (the scan) and searchable text (the OCR), it gives a terrible conversion as you end up with both interleaved and neither is much use on an eReader... if your other books were also PFS or conversions of this type then your time taken is expected as each page (in scanned and assembled PDFs) will be treated as a graphic rather than text...
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