I'll probably get flamed for saying so, but I'd keep the source files around if I wanted to make changes, but actually convert the file to PDF before loading it on to the device.
You can choose any font, any font size, any justification, etc. You can export the PDF through Word or any other modern word processor. Just be sure to follow
Sony's instructions on setting the page size, etc., eliminate margins, and so on beforehand, and be sure to make it has the font size, and other settings you like before exporting, because you'd need to go back to the source to make changes.
Links should work (--or they do if exported though OpenOffice; I don't use Word--), possibly TOC depend on how it's made, metadata is possible (--you may need to add some through calibre though--), etc.