North to South in 4 weeks

It seems pretty simple - a 21 day pass works very well from Asahikawa down to Hiroshima and back to Kansai, yielding you well over 30,000 yen in savings, and more if you add some other worthwhile side trips to Himeji, or a day trip to Nikko before going to Hokkaido, etc. For your last week or so in Kansai, you could use regular tickets to travel around the area, or there is a good [regional pass] you could use. For Koyasan there is also the Koyasan World Heritage Ticket - I think you can enjoy yourself more on your own freedom and schedule without joining some tour.
Aside from, Kyoto, don't miss Nara either, and Kobe is worth at least half a day too.

Thank you Toraneko. I needed that validated by someone. So even if I have days, I don't step on a train, the 21day pass repays itself.