I've looked into several different ways to accomplish this myself. There is no perfect tool.
If all you need is text then you can get away with using libprs500. It only really handles text and does not do a good job with tables, images, etc.
If this database creates the PDF and you can set the page size then I would recommend keeping them PDF and just set the page size. The SONY reader DOES handle PDF just fine and are very readable, they just have to be created for the READER to look good. The problem is most PDF are created for letter size(8.5x11") or larger.
There is one that I've found to be the best tool for reading PDF. I tend to read a lot of tecnical books with tables, charts and images. So keeping the layout is very important to me.
This tool is written for the SONY reader and is a tool called PDFLRF (note not the same one listed above)
https://www.mobileread.com/forums/showthread.php?t=13135
It turns each page to an image then enhances the image to bold the fonts and remove extra white spaces.
This of course has the drawback of making the LRF(PDF) much larger since it turns the text to an image.
Hope this helps,
=X=