I arrived from Tokyo around 9pm and had all-day Tuesday and Wednesday in the small city. I found some similarities with Kyoto, but it's much smaller, so don't come here thinking it will be the same. It's not (I spent a week in Kyoto and there was plenty to keep me occupied).
The Mitsui Garden Hotel was a steal at $65/night, and great location. Just a five-minute walk to there Omicho morning market for sushi, beef, fruits and more. I ate it all including urchin, a kaisen-don bowl , grilled beef, plums, and made to order sushi. I visited a few historical buildings, food stores, museums and walked along the river in the "geisha district."
The Castle and Gardens were hot. I ducked into the Museum of Modern Art (see the swimming pool) to cool off. Then a tasting at Fukumitsuya which has been brewing sake at this location since 1625.
The "samurai district" has great Edo-era architecture and I found a great izekaya. though no English menu (online translation is a life-giver). There are also a few small shrines and temples you can visit near the city center.
Three nights and two days was plenty. It took a good three hours to get from Haneda to Kanazawa Station (no advance JR reservations needed). Very walkable and good food scene, nice old architecture, and a bit off the beaten path.