kansai historical itinerary + hakodate

Dear Mari,
I am graduate student in history who is beginning a language course in Hakodate on the 7th June. I have extra time prior to the program and I had hoped to make an 7-day itinerary to correspond with your 7-day pass. Impecunious student that I am, I would prefer a sleeper-train that did not incur extra cost and which would allow me to arrive in Hakodate by noon or so on the 7th June. Do I need to make reservations prior to arrival?

I had also thought of doing some sort of itinerary in Kansai to get a fuller sense of the country. The obvious destinations are Kyoto and Nara, but it strikes me that I won't have time to fully explore these places with so little time, and that I might make better use of the pass by visiting other places. Do you have recommendations that work well with the rail-pass? Or are Kyoto and Nara really the places to go, even if I might have opportunity to visit them later? I like history and hiking and am not shy of more obscure sites if they have merit.

Thank you very much for your help!

Jesse