Is there a pass that's worthwhile for our trip?

I’m travelling around Japan in May with my partner for three weeks, and feeling REALLY overwhelmed by the train system / logistics!

Our itinerary is:
• Arrive in Tokyo - 5 nights there, with a day trip to Kamakura • Overnight stay in Hakone • Hakone to Nagano - 3 nights in Nagano, with day trips to Matsumoto and Obuse • Nagano to Kanazawa - 4 nights in Kanazawa • Kanazawa to Kyoto – 7 nights in Kyoto with day trip to Osaka and Uji • Travel back to Tokyo

According to the www.japan-guide.com rail pass calculator a JR Pass won’t be good value. (It estimates our travel costs will be approx. 52,500 YEN, and the 21-day pass is about twice that.)

My main questions are:

1) Is there any combined pass that WOULD be good value for this itinerary? The Hokuriku Arch Pass seems like it would be great, except that it’s only for 7 days. Would it be worthwhile (or even possible) to purchase one 7-day pass, then purchase another for the following 7 days? Even if a pass doesn’t save us much money, the convenience is really what I’m after. (I obviously don’t want to pay lots MORE for the pass, though.)

2) For most local travel around each city, will we be able to pay using an IC card to ‘tap in and out’ at ticket gates or on buses, rather than buying individual tickets?

3) Do we need to worry about booking any trains in advance, or is the availability good on the day during May? (We are travelling AFTER Golden Week is over.) Do you save any significant money booking in advance?

I’m finding the prospect of it all pretty stressful – travelling around a lot like this is quite out of my comfort zone. I’d appreciate advice on how to make it as easy as possible while still being cost-effective.