Advice on tickets/passes for 21 days (Tokyo>Hakone>Nagano>Kanazawa>Kyoto w/ day trips too)

I’m travelling around Japan in May with my partner for three weeks, and feeling REALLY overwhelmed by the train system / logistics! I'd love some advice on passes/tickets and how to make things as stress-free as possible.

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 trips 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, and the 7 after that? Even if a pass doesn’t save us much money, the convenience is really what I’m after. It seems like this one would cover a lot of the local travel in Tokyo too which might help make it worth the cost - or am I mistaken? (I obviously don’t want to pay lots MORE for the pass vs. buying stuff separately - I'll pay a bit for convenience, but not stupid amounts.)

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? Or do you still need to go to a ticket machine and buy? (Seeing lots of stuff about base fares and extras!)

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, like you do in the UK?

I’m finding the prospect of it all pretty stressful – travelling a lot in a new country is quite out of my comfort zone, I'd usually stay in one city and walk most places.

I’d appreciate advice on how to make the journeys above as smooth as possible while still being cost-effective.

(It doesn’t help that I’m used to trains in the UK which are incredibly unreliable and overpriced, which is probably making me more worried about it all than I ought to be!)