1& 2) I liked the location of Haneda (HND) - a short cab ride or monorail into town. The airport itself is pretty uninspiring, it's clean, it has the basics, but that is about it. Customs / immigration was speedy, bags took a little while to appear.
3) Personal preference, I came back to Tokyo, as I didn't have the option to fly home from Kyoto directly.
4) Depends how much you will be using it, hyperdia.com will give some idea of the cost without a JR pass for you to compare.
5) I wouldn't opt for 3 nights in a Ryokan, I think 1 is enough - especially with potential jet lag, as you don't have the option for a midday nap at a ryokan. I stayed in 2 ryokan type places, but neither were in Kyoto.
6) I really liked Nara, and on the way back from there to Kyoto stopped at Fushimi Inari-taisha which I thought was very interesting.