How to automatically convert academic papers (PDF) for reading on a Kindle

I got a Kindle for Christmas and I'd like to read some academic papers on it. Almost all of those papers are in either PostScript or the PDF format and made for A4-sized paper. See the example here.

Sending the PDFs to my @kindle.com address (with "convert" as subject) doesn't work because the converter fails to recognize the two-column layout that's so common for those kind of papers and treats it instead as a single column, mixing paragraphs from both columns.
Same goes for Calibre unless I'm doing it wrong.

I can certainly read the PDFs on my Kindle in landscape mode but the small font is hard to read and zooming in requires me to pan in all directions because of the column view.

So my question is: Short of converting the files manually, are there any solutions you can think of?

Edit:

The Calibre manual has a detailed explanation on the difficulties of converting PDFs to other formats.

To re-iterate PDF is a really, really bad format to use as input. If you absolutely must use PDF, then be prepared for an output ranging anywhere from decent to unusable, depending on the input PDF.

That pretty much sums up my experience. I've got a solution in mind but it involves some programming of OCR / Document layout analysis but I'm hoping to avoid having to dive into that particular field. (I'd rather spend my time reading, so any and all suggestions are welcome.)