- Is there any kind of alliance to be had with Albertine Press? ( http://albertinepress.com/about.html ) I'm not sure what the angle would be exactly, but they're just a few blocks away, and might have equipment and expertise that would allow for a more interesting kind of print-on-demand than the Espresso printer. And if bookstores are increasingly becoming fellow travelers with letterpress printers and vinyl shops and so on, maybe there are strategies in common.
- Others have mentioned affiliate fees. If book stores are no longer efficient ways to store and deliver books, but are still great ways to look at and play with and explore books, is it possible to fully transition to a book showroom instead of store? How would the business change if you were no longer thinking in terms of inventory, but only in terms of sample copies? You obtain exactly one copy of the very best books that fit comfortably in your space; the customer collects ones they like; and then they're scanned at the front desk, searched online, and the cheapest available copies of the quality they request are shipped to their address. So customers are getting Amazon prices (or better, because you might be better at running the search than they are), but the experience of discovering physical books. You could pay for it either with affiliate fees, if there's a program that works, or with a surcharge.
If you went down that path, your focus on the supply side would change from acquiring second-hand books, to finding really interesting ways to discover books. For example, shelves where you can flip through the top-ten favorite books of Bill Clinton, or Neil Gaiman, or Natalie Portman, or David Foster Wallace. Cyberpunk shelf curated by Neil Stephenson (with a blurb taped inside each cover if he'll write one!). Law & Tech shelf curated by Larry Lessig. Books by TED presenters. Make it so poking around the store is itself a learning experience.
Good luck -- I hope you manage to find someone, and their ideas are better than mine.