I also have a lot of PDF files where the text is just too small to read on my Pixelar Hanlin. It's easy enough to convert to text (through Adobe Acrobat, or even copy & paste into Word) and then save in RTF, which is at present my favourite format because you get 5 different font sizes. But the PDF to TXT conversion sticks a paragraph break (a hard line break) after ever line (A4 formatting). This introduces line breaks in the middle of lines when you reformat the page to 9cm by 12cm. I do a global search and replace to get rid of ALL paragraph breaks.....then have to put up with a book that contains only a single paragraph. Not ideal!
I have also tried converting from PDF to EPUB and MOBI using Calibre, but the special characters cause some formatting problems (I read mostly in French and German) and I get books with spaces in the middle of words. Presumably there is some kind of text editor for MOBI where I can do a global search and replace to get rid of the unwanted spaces?
The final problem I have with converting PDFs is that when they are in Russian, the .TXT conversion is unreadable. Presumably there needs to be some code to tell the text displaying software which character encoding is being used. Converting to .DOC in Word is the best solution I have found, although as I said I prefer RTFs. I don't know how to get the character encoding right in RTF.
Pixelar are offering a new firmware download that offers PDF reflow (what's that?) but I'm wary of it because then you lose the Japanese character suport. I read a bit of Japanese and don't want to lose that functionality.