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I agree with JSWolf
I’ve had similar experiences of scrambled text with converted PDF books. Unfortunately, I don’t think there is a simple fix.
The books that gave me the type of problem you described had each chapter start off with a large drop character. All of the scrambled lines were from the first page of the (PDF) chapter. In searching for a reason and hopefully a fix, I found that, using Adobe Reader, I could not cleanly highlight and block copy the first page a chapter. Some of the text would highlight and some would be skipped. A block copy of the second or any number of subsequent pages would highlight and block copy as you would expect.
My brute force fix for this scrambling problem was to use a text editor (I use Sigil) to unscramble the ePub text via cut - and – paste, and using the PDF original as a guide. It’s a crude solution, but it’s the only fix I’ve found. If it was more than one page per chapter, I wouldn’t have bothered.
I refuse to read PDF books and have not personally found a PDF to ePub conversion that would produce acceptable results and didn’t require some post conversion tweaking. Over time I have worked out a system that gives me marginal, by my standards, acceptable conversion results, but I really really have to want to read the book to go through the process. I usually just pass and hope an ePub version becomes available.
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