So I have the JR rail pass and I am studying the rail timetable, but I cannot figure out how to get from Kanazawa around the alps up to Matsumoto. Can I connect at Itoigawa to a train up to Matsumoto? Or do I have to circle all the way around north/northeast to Nagano first?
Thank you so much any advice appreciated!

www.hyperdia.com can give you all the connections.

we took a train from Matsumoto to Kanazawa. Direct, I believe.

Check hyperdia though.

The easiest connection is through Nagoya...a single change in Nagoya from the Shirasagi to the Shinano. You can make better time if you plan carefully and go through Nagano though, but that requires at least 2 connections. www.hyperdia.com will give you your options, though only 5 at a time...just play with the time to get more options.

There is a bus, but your JR Pass is not valid for that. http://www.alpico.co.jp/access/expre...wa/info_e.html

Itoigawa would be out of the way. hyperdia shows the northern route from Kanazawa to Matsumoto goes thru Naoetsu. To get from Itoigawa to Matsumoto the route also goes via Naoetsu.

That northern route, as KimJapam mentioned, would involve a couple of connections. Also, it would involve an hour and a half on a JR local. I think I might prefer the one-stop better ride on limited express trains going via Nagoya.

I took the train from Matsumoto to Nagano once. I was headed to Tokyo but decided to drop in on the magnificent Zenkoji (a 7th century Buddhist temple) in Nagano. This is easily done by a short bus ride from the station (could walk) and then a short walk. There is a crawl path under the temple that is interesting at the beginning but a bit spooky towards the end.

South of Nagano the train rides a ridge and there is a great view of the valley with the city. It would be on your left as you headed south to Matsumoto.