I am too in academics and read a lot of research papers which are in pdf format, what I have found is multicolumn pdf do not render ok, multicolumn do not reflow the way you want them, and text is way too small if you want to retain their aspect ratio on the screen, there exist few tools in these forums but they are still experimental.
So in my opinion single column text based pdf just render fine without any intervention, but graphics, tables and graphs are just not good.
Pdf file format is not meant for 6 inch screen.
If you are using sony ebook library than you can read this thread on how to
make collections.
https://www.mobileread.com/forums/showthread.php?t=15797
If your primary concern is pdf reading than iliad with full screen is the option or you can wait for eslilk from foxit software to be released in few weeks.
I use calibre and it does make collections of all newspapers rss feed.I honestly dont know how calibre does it, may be via tags?
For experiment I am using trial version of foxit pdf creator to generate pdf files from my existing pdf and surprisingly it works fine with pictures, tables and graphs but unfortunately not for multicolum pdf.
I have decided to wait for eslick their link is
http://www.foxitsoftware.com/ebook/