For each book they store its exact location in the torrent files. You can see on the book page, e.g.:

collection “ia” → torrent “annas-archive-ia-acsm-n.tar.torrent” → file “annas-archive-ia-acsm-n.tar” (extract) → file “notesonsynthesis0000unse.pdf”

But probably you should get it from the database dumps they provide instead of hammering the website.

So you come up with a list of books you want to prioritize, search the DB for torrent name and file to download, download only the files you need, and extract them. You’ll probably end up with quite a few more books, which you may index or skip for now, but it is certainly doable.