Was Karuizawa part of the original options? It's just a stop from Nagano.

Will you be visiting Shirakawa-go as part of your Kanazawa stop? Kanazawa also have some hot spring spots if you like that kind of stuff, although in September it might be not the right time haha.

I don't think you can get off at any stations between Kanazawa and Nagano using JR Pass. They are not part of the JR lines, even though the Hokuriku Shinkansen runs through them.