How to OCR a 2 column document (textbook) and not have the text from the two columns combined

As Bernd, said, this is not possible IN Acrobat.

But it is possible depending on how you scan the page. 

First off, forget about doing the scanning from within Acrobat. Just find the software that came with your scanner and run that directly.

Some scanners can scan two different regions sequentially (as if you have two (or more) photographs on the glass). If you can do that, great. otherwise, you just have to run the scanning process twice (or more depending on the original page's layout).

Set your scanner to save each one in a convenient place (Desktop?) and save in the TIF format. After you have both columns scanned, than open each of these documents in Acrobat. Since they are in the TIF format, they should both be converted to PDF and then OCRed automatically. Once complete, you can copy out the text or export as a Word document.

Yes this is more tedious than if it could be done within Acrobat, but it's better than trying to match up the two half's as you've been attempting.

As long as I have your attention, here's a blog I wrote for Adobe on how to get better scanning results.

http://photosbycoyne.com/Gary's_Help/Scanning/clean-scanning.html

Good luck!

Not possible.