PDFs are pretty much write-only, and in my experience (with Adobe Acrobat-based devices) reflow never works very well. As long as you use a sane text-based ebook format, Calibre can handle conversion to other formats.
So I recommend converting into - if not EPUB, then maybe just a clean HTML (with all the links retained - readers that support HTML should have no problems with links between file sections).
then maybe just a clean HTML
Yes, some readers (e.g. Pocketbooks) can handle HTML, but even the latest Sony readers cannot. Kindle does have HTML support "via conversion" but I don't know if it can correctly convert 600 or so interlinked documents.
I've been wanting a printable copy of the sequences to read through in meatspace. I wrote a quick scraper and uploaded the results here http://pwnee.com/Sequences/list.html
Inter-linking doesn't work, but I just wanted a printable version anyway.