Best way to get from Nagano to Hokkaido?

Hi, I'm Ling, a wildlife photographer from Singapore.I'm having a little trouble with the maps and rail network of Japan.

I would like to know what's the best way to get from Nagano to Hokkaido? by flight or train?

Nagano: i will be visiting Shiga Kogen and Karuizawa

Hokkaido: I will be visiting Kushiro and Rausu.

Looking at the train lines here http://www.japan-guide.com/e/e2361.html
It's possible to take the train from Nagano to Kushiro right? All with the Japan Rail Pass?
Is it possible to take a night train?
After days of research online, i somehow found out that the journey is gonna take 11hrs? I forgot where i got that info. I'm really getting a little dizzy from all the names and maps.

Any help will be very much appreciated! thanks!

The fastest option is probably by shinkansen to Tokyo and then by direct flight to Kushiro.

Another option is to fly from Matsumoto Airport to Sapporo and then take another flight to Kushiro.

About domestic airfare:
http://www.japan-guide.com/e/e2364.html

Or take the train via Omiya, which would be a 15 hour journey. Fully covered by the Japan Rail Pass if you use daytime trains. But most night trains are not fully covered:
http://www.japan-guide.com/e/e2356.html