If I want to buy a book, i'll go to Amazon and buy it. With kindle, i'll have it in 10 seconds. If its not available on Kindle with Prime i'll have it next day. You can't compete with Amazon. So its not worth trying.

If you want to run a remarkable book store today, don't sell books. That's a loosing battle. This is where i'd start if I was trying to think of ways to innovate in this space. I'm sure you're familiar with Porter square books. They for instance have built a pretty remarkable community around the store with book clubs etc.

Other then that, i'd like to say good luck! I live in Boston, so i'll try to visit the next time i'm in the neighborhood.