JPRail.com is also very helpful for building itineraries. You might want to take a look at this itinerary if you like trains http://jprail.com/category/travel-in.../2017-hokkaido
JR Hokkaido also publishes some model courses http://www2.jrhokkaido.co.jp/global/...del/index.html

There are special lavender season & Biei trains for the Furano area if you are visiting during that time frame
http://jprail.com/trains/sort-by-typ...-railways.html

Bus Map
http://www.uu-hokkaido.com/corporate/sharibus.shtml Page is for Shiretoko, scroll down for Hokkaido
JR Hokkaido map
http://www2.jrhokkaido.co.jp/global/english/rmap/

You can also fly between CTS and some of the smaller regional airports like Memanbetsu and take the bus to Shiretoko or fly to Kushiro to catch a bus from the airport if there isn't a well timed train route or highway bus.