I'm an academic like you and I read technical PDFs on my Sony PRS-505. My favorite way of dealing with them is to use
soPDF (or
PDFLRF if they're scanned,
PaperCrop if they're multi-column) to remove the whitespace margins, and cut the text blocks into reader-sized chunks.
I find I can read just about anything that way.
Converting to another format does not work well with technical material. Either keep it in PDF format, and tweak the PDF to make it easier to read on your screen, or convert the PDF pages to images, and tweak the images to fit your screen size.