Making our way down from Hokkaido to Kyoto

You can see one possible way by train on:

http://www.hyperdia.com/cgi/en/search.html?dep_node=NISEKO&arv_node=KYOTO&via_node01=&via_node02=&via_node03=&year=2015&month=03&day=12&hour=06&minute=00&search_type=0&search_way=&transtime=undefined&sort=0&max_route=5&faretype=0&airplane=off&ship=off&bus=off&privately=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7

It is taking a train from Niseko to Hakodate though, not by bus. If you have not exchanged your vouchers yet you can do it at Hakodate, but you'll have to pay out of pocket to get to Hakodate. The above method has you leaving very early though to do it. There is also one error in it - you are unable to take the Nozomi bullet train from Tokyo - so correcting for that, there is a Hikari bullet train leaving at 4:33PM and arriving in Kyoto at 7:11 PM.

One could certainly say you are getting your money's worth for that Pass, but you are murdering a whole day on the train with little to do. It's strange you didn't choose to fly. You could go from Sapporo to Osaka in only about 2½ hours for as low as 4900 yen per person on Jetstar.
http://www.jetstar.com/jp/en/home