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Hi,
I have the same problem, but for a sony reader. In fact, the prs600 does pretty good with pdfs, even with two columns. increasing font size does a reformating that is not pretty but readable, and the columns are not mixed. The problem is just when there are figures that take the entire width of the page. Then there is no possibility for larger font.
The solution I have found is to abandon pdfs in this case: if the journals you are reading have a web site, they often also offer html version of the paper, and this is quite easy to transform into epub. And they look perfect this way.
I am currently fighting with the "recipe" features of calibre (and my ignorance of python) to have it upload automatically my favorite journals directly in the format I want.
Hope this helps,
V
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