Hi there,
Cool itinerary! You will basically see every Island of Japan, including Kyushu and Hokkaido! Very impressive!
Now I can certainly imagine that it may be somewhat hard to find the right JR Pass combination here.
You could go for a 2 week pass and travel to Hokkaido, then rent a car whilst you are there. Some parts of Hokkaido are better visited by car while others are best reached by train. Here is a complete map of all train stations in Hokkaido. I would suggest writing down what you wish to see, than see if you can reach it by train or not and on that make the decision if you go by rail or car.
The same kinda applies for your travel to Kansai (Kyoto/Osaka area) train travel in the area is not very expansive and you may be better of with a 2 week JR Pass if you stay local.
Of course you could just buy two 3 week passes and live by the day without having to worry about having to buy train tickets. The upgrade from a 2 week to 3 week pass is relatively low in comparison.
A last option I would like to point out is going for Green Pass (First Class). First class trains in the north of Japan are really really really nice and comfortable in addition they include a free drink when you enter. Than you could take a 1 week pass for your travel past Tokyo and try to reach Kansai withing its period of use.
I hope this helps!
Daniel
