I ran your test .pdf (the AJOG Opinion article) through Docudesk's PDF to LRF conversion tool (free OS X tool available at
www.docudesk.com) that will automatically reflow PDF's into LRF (and other text formats too for the pay version). There are several text detection/reflow modes available, I used the "automatic" or default one. I'm afraid that the results weren't too good. The original PDF was not authored to allow easy/coherent reflowing of the text so this automated conversion tool didn't put all the variously placed text blocks together into a single stream of text quite right.
You can download Sony's free connect software to preview this .lrf that I generated to see what it might look like on a Sony Reader. If you're an expert in using Adobe's programs (expensive software at that) to re-format/reflow PDF's, you might be able to get a nice clean PDF -> LRF conversion. Or you can try playing with the Docudesk converter's various settings. This however is likely to get pretty time intensive as you'll have a great deal of manual trial and error to get the results you want if your goal is to replicate the paper completely.
If you only want the text of the paper, you could try just copying all the text in a PDF and pasting into a word processor/text editor and doing some quick easy cleaning up of the formatting. Though in this case, you'd lose most of the formatting that would be especially important in replicating charts/tables and would lose any graphics/graphs. And there is no way to really automate this due to the editing you'd have to do.
RasterFarian is probably your best bet at this point though if you want a fast/automated way to re-create the PDF with all it's carts/graphs/tables perfectly in a more viewable form on the Sony Reader. Only downside is larger file sizes as each page is a graphic instead of text/symbol data.
Dave