Hi there,
You have a couple of options here,
Personally I would start using the JR Pass the moment that you leave for Kamakura and on to Osaka. This because local travel in Tokyo is relatively cheap and the JR Pass is best suited for the longer distances and up to Nikko it is certainly the way to trave.
After Nikko you can either fly or take the train to Hokkaido. Taking the train to Hokkaido with the JR Pass is by far the most economic option but will take a long period of time. Travel from Nikko to Sapporo takes about 10 hours by train so it is a very long ride. An airplane will get your there in about 2-3 hours but prices can vary a lot and it is hard to say how much it will cost.
Personally I did the trip by train to Hokkaido last March, I decided to take the train as I would just use one day of the pass and have the other days left and could go where I wised without having to pay any additional fees. You can also plan a stop or two on the way to Hokkaido if you feel the trip is too long in one go.
For the rest, I really like your plan and I hope you have a great time in Japan!
-Daniel