Itinerary Check: 13 October days in Japan

Greetings, everyone!

My parents and I are planning to head to Japan this October, 2018. We've visited Japan quite a few times before, but usually just within a specific area (Osaka only, Tokyo only). For our trip, we're planning to visit numerous locations around the country (that means, Japan Rail Pass--7 days).

I'd love to hear some feedback/recommendations on our itinerary!

Day 1: Arrive in Osaka, check in accommodation, spend the night.
Day 2: Osaka city area.
Day 3: Kyoto for the Jidai Matsuri (October 22), other Kyoto areas.
Day 4: Activate pass, Kanazawa.
Day 5: Takayama.
Day 6: Shinkansen to Hakodate, spend the night there.
Day 7: Hakodate/Onuma National Park, head home to Osaka.
Day 8 (Saturday): Hakone
Day 9 (Sunday): Tokyo
Day 10: Undecided. (Last day of JR pass)
Day 11: Day trip to Himeji Castle
Day 12: Other Kansai areas (Nara, Kobe, Kyoto, etc.)
Day 13: Head home.

We've got great accommodation within walking distance of Shin-Osaka station so almost all of the areas will be day trips (except Hakodate, my dad really wants to visit Hokkaido so we gave that to him). We're quite fine with taking the first train then the last train for most trips.

Our main concerns is that one undecided day and where to go on the weekend. We love going off the beaten track (not too off, though!), and we can switch around destinations if ever.

Again, I'd love to hear any thoughts on our trip! A big thanks to Japan-guide and the community here! You've all been so helpful.

You dont have enough time for hakodate going by train both ways.

Takayama to Hakodate is 7.5 hours plus transfers and Hakodate to Osaka is 7.0 hours plus transfers. So a single overnight there will not be realistic.

The rest of the Itinerary is fine.

you have a free day, so use that for Hakodate.

Also Hakone and Tokyo and between Takayama/Osaka and Hakodate, so you could places then before and after Hakodate, reducing travel times to and from by 2 hours.

Hakone should not be done from Osaka if you have Tokyo in the itinerary.