Hokkaido, Tokyo, Kyoto, Akita travel between Dec 22 and Jan 31: advice re combinations?

We are 4 travellers (2 adults, 2 13 year olds) travelling in Japan for more than a month, and hoping for advice on how best to book train tickets, maybe using the JRPass or regional tickets. Here are our planned routes and dates:

22 Dec: Sapporo to Furano
6 Feb: Tokyo to Akita
20 Feb: Akita to Kyoto
29/31 Feb: Kyoto to Tokyo

Can anyone advise which the best tickets and passes might be to purchase and how to reserve seats? Any scenic or special routes we should consider while we're in these areas? Will the JR or regional passes also allow train travel within metro Tokyo and Kyoto, or between Hokkaido stops? And when should we book these?

Thank you very much -