Every time I went to Kyoto, the first place I'd head to was the Maruzen bookstore.
My only piece of advice to you regarding Kyoto is, if you're driving, make sure you know the international symbol for 'no parking'. My first visit there I was dropping a friend off at the train station and had some time to kill. Arrived early in the morning (like before 6am) parked in the central city (where there were plenty of other parked cars) and spent the next few hours wandering around.
When I got back to where I left the van (with all my friend's luggage), it just wasn't there. I checked the landmarks I had used to orient myself, was pretty damned sure this was the place but then spent an hour wandering up and down looking for the van.
Then I happen to look down and see a large piece of paper taped to the ground with both Japanese and English. "Your vehicle has been taken to the Gojo-dori Police station." Great! Spend another 30 minutes trying to find it only to discover I had parked right outside it.
Spent all the money I had for book buying to get my vehicle back and it still wasn't enough! Had to phone my Sensei to vouch for me and promise to pay off the remainder at my local police station!