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Abbyyy Finereader is a software program that you purchase. I convert the PDF to html files and then covert them to epub/mobi. Abbyy's a bit pricey, but I personally use it enough to justify the cost.
I don't know about converting PDF files using Calibre - you may want to check the workshop or Calibre forums on MR about converting PDF's.
Just be prepared for a very large file from 1dollarscan (mine with only normal OCR are usually around 350,000 KB). Your high quality scan will probably be larger and just might choke Calibre. But hopefully someone will have experience with this and be able to help you more.
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