I have run into a very similar problem with my 2850+ book collection. I have used either "acid-free" poster board or, surprisingly enough, the dust-jacket covers to create a barrier between the books and the books shelves.
I don't mean using the dj cover material to actually protect the dj (although a good deal of my books are protected in this way), but to line the sides, backs and bottoms of the shelves and bookshelves.
The dust-jacket covers are the best in protecting your books, although more expensive. You can order a pretty good supply of them on-line.
My books are all housed on all wood, all oak, untreated books shelves - but I still use a liner; just to be safe.
"There are two motives for reading a book: one, that you enjoy it; the other that you can boast about it."