Japan for 6 weeks

I am traveling in Japan for 6 weeks during the World Cup. I would like to know the best options in terms of JR passes/regional passes for the trip. This is the rough schedule of the trip.
We will be there from the 20th of September to the 3rd of November. We know we will most likely need to purchase at least one 21 day pass and possibly a 7 day pass but when would it be best to begin the pass as our trip extends longer than the passes.
Tokyo - Yokohama (3 days)
Yokohama- Toyama (5 days)
Toyama - Takayama (2 days)
Takayama - Shin-hotaka ropeway (1 day)
Matsumoto-Kamickochi (1 day)
Matsumoto- Kobe (3 days)
Kobe -Kyoto (2 days)
Kyoto - Okayama (2 days)
Okayama - Hiroshima ( 2 days)
Hiroshima - Fukouka ( 2 days)
Fukouka - Beppu (3 days)
Beppu - Tokyo
The final 2 weeks are mostly in Tokyo, Yokohama and Osaka.