Hi everyone,

I will be in Japan for 14 days next month.

This is the plan:
Fly into Narita-go to Tokyo for 3.5 days
Tokyo to Matsumoto on the Azusa for 1 day
Matusomoto to Takayama by bus 1 day
Takayama to Shirakawa-go by bus and back to Takayama by bus with an overnight in Shirakawa-go
Takayama to Kyoto by train with 1 night in Kyoto
Kyoto to Onomichi by train to do Shimanami Kaido bike ride across islands
Onomichi to Kyoto by train with 2 days in Kyoto and fly out of Osaka

Should I get a JR pass or book each ticket separately?

Thanks!!

spend a day in onomichi before biking on.

I computed the fares as follows using hyperdia.com:
Tokyo to Matsumoto 7100 JPY
Takayama to Kyoto 10,260
Kyoto to Onomichi RT 18520 for a total of 35,880.
The 7 Day JR Pass is 29,110 so if you do that traveling within seven days it would be a good investment. A 14 Day Pass is 46,390 so would not be needed unless you add some other destinations.

Figure the cost of the two airport transfers plus a few JR locals in Tokyo to be about 5500, so just pay as you go for that.

A few suggestions (which you likely have already considered):
Plan a stop in Kamikochi for a few hours on the way to Takayama. You could also stop for a soak at Hirayu Onsen on the way. If you aren't planning to make a stop on the bus ride from Matsumoto then I suggest just taking JR around to Takayama. The Best Western would be my choice in Takayama, clean, comfy, very close to the JR and bus stations. You could skip Hida no Sato in Takayama because you are going to S-go. Leave luggage in Takayama and travel very lightly for the overnight in S-go. Leave stuff in Kyoto for the overnight in Onomichi.

You are moving around a lot. For that reason I suggest you consider taking time from Tokyo at the beginning and adding it to Kyoto at the end.

You could go on from S-go to Kanazawa instead of returning to Takayama. Maybe better: go from S-go to Kyoto and that would free up a night to use in Onomichi and do as Ken suggested above (IOW two nights for Onomichi).

Thank you for the great ideas! I didn't think about getting a pass for just 7 days. That works out perfectly!

And I'll try to expand our time in Onomichi. thanks!

I loved Onomichi - the temple walk....and the movie Tokyo Story was set there - they also have a film museum.....I was planning only half a day there but ended up spending the whole day.