This question is directly for Jonathan (seeing as he made the site). I’m an author (or at least, an “aspiring” author) who has been researching different ideas and “things” all over the place & your Library of Babel has brought me great inspiration (as I’m sure the original novel did for you ;D).
Anyway, before I give too deep into the idea, I just wanted to know if you were okay with me using your site in the novel and if you are, what specific things you would have me exclude or change.
Since Jonathan isn’t around very often, I feel I can answer this for him. The Library already contains everything that can ever be written, including your novel. This also includes all versions of your novel, no matter how little it is changed. A version could exist where the main character’s name is “Mathew” or “Jonathan” or “Hdqwtxpl”. It contains versions with typos and without. 😉
Having said that, the contents of the Library cannot be subject to copyright. Think of it like a fancy number generator (like a very giant dice). If you roll it, there’s a 1 in 10^4677 chance it will land on a singe page of your book. Roll the dice again for page 2, 3, etc. This also means that it can contain full books, such as those that are still under copyright. For example, here’s the first paragraph of Harry Potter and The Sorcerer’s Stone, appropriately on the first page: https://libraryofbabel.info/bookmark.cgi?harry_potter_sorcerers_stone_first_paragraph
As you can see, it doesn’t matter if a work is protected by copyright or not. The Library simply spits out random letters until eventually they form pages that make sense. Jonathan can’t own anything it generates, so he can’t stop you. If he could, he would own every piece of art and literature that will ever exist. Feel free to write whatever it is you wish, as long as it remains legal (not plagiarizing copyrighted works).