The most important decision is the format. PDF support is pretty ubiquitous, but it's not reflowable (i.e. can't adapt to different screen sizes and user-adjusted fonts automatically), which looks bad on devices that have screens of different size than the size encoded in the PDF. Many devices implement some form of PDF reflow, which may work well for simple-layout PDFs (with no pullquotes or columns). There's EPUB, a good reflowable open-source XML-based format, but it has its downsides too: not all ereaders support it, and, as I gather from the wikipedia page, the situation with linking is unclear -- which is important because the sequences are heavily interlinked. There's also CHM (Windows help file format) which is both reflowable and linkable since it's based on HTML/CSS, but, as far as I know, few ereaders support it. Based on my own experience, I strongly prefer EPUB. However I have no experience with its linking support. I'd first try a linked EPUB and see how well its linking works on popular devices, or, as a second option, try a simple, sinlge-column, no-pullquotes PDF encoded for a 6-inch screen and see how well it reflows on various readers.

Once you've harvested the text it would be straightforward to make a PDF, but I'm not sure how many ereaders support that format.