Alex_d's PDFrasterFarian made the big difference for reading pdfs. I read a lot of academic papers and thesis after the conversaion, and they work wonderfully in the quarter-a-page mode for 2 column formatted papers. Checkout this thread:
https://www.mobileread.com/forums/showthread.php?t=9106
And yes, you are right, pdf securities must be removed before they can be properly processed.