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Even if you get it to work, VERY SLOWLY, the Table of Contents may be larger than most entire books, especially when displayed on an small screen.
Certainly there are topic areas which lend themselves to creating books by themselves. At least in the Sony Readers you can create Collections, this sort of thing may be helpful.
Make sure the links don't point outside of the device, as some devices are not connected to the internet all the time or accept references to the web.
The Harvard Classics, which your project sort of reminds me of, takes 50 paper books and the ereader files keep the same number of books.
Links are case-sensitive in epubs, so you will have to watch for that too.
You might try just copying and pasting articles one at a time into Sigil, making sure to insert chapter breaks so that some readers will not fail because the sections are over about 250k.
You could use something similar to HTTrack to get the whole web site on your computer, so you have access to all the bits and pieces as you construct your book.
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