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PDFscissors allows you to select the columns using a "select top left, bottom right" approach, two or 3 times for each column on a page. But if the number of columns per page varies then, no, it will not work. It is actually a java online app so you could try it. How it works, select col 1, select col 2, select col x.... and then do the cutting. So basically it grabs col 1, moves to col 2, grabs it, then 3 and then moves to the next page. So c1 is page one, c2 is page 2, c3 is page 3, and then c1 from page 2 becomes the new page 4, etc....
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