If your book looked that crappy after conversion I doubt it's even a multi-column issue, it's probably a source with some OCR. If my guess is right there's basically nothing you can do except load it up in OCR software like ABBYY Finereader or Acrobat Professional - but that's going to be a lot of work.
Did you read the sticky at the top of the forum?
https://www.mobileread.com/forums/sho...d.php?t=118605
I don't believe that is written in an overly complex/technical manner, but if it is let me know which parts are confusing and I'll try to make it simpler.