Initiating Travel Plans!

Good morning,

I am starting to put together an itinerary to make the most of our visit to Japan scheduled for Feb 12-28th/2018.
I'm a little confused over what the JR pass covers, and what it doesn't!
Here is our wish-list so far:

Tokyo 2nights (arrive 13Feb, HND airport).
Nikko 1 nights Feb 15-16 (Tosho-Gu Shrine, Hike through Cedar Forest).
Hakone 2 nights Feb 16-18 ( Ashinoko Lake cruise, Cable Car, Onsen).
Takayama 2 nights Feb 18-20 ( Hida Folk Village, Markets & Food).
Hiroshima 2 nights Feb 20-22 (A-Bomb Dome, Island of Miyajima, Cable Car to Mt Misen).
Kyoto 2 nights Feb 22-24 ( Himeji Castle, Kinkaku-Ji Temple, Geisha District, Fushimi Imari Shrine).
Osaka 2 nights Feb 24-26 (Food! Day-trip to Iya Valley? is that far?).
Tokyo 2 nights Feb 26-28 (rest before long journey home).

Does this itinerary work with a JR pass? Obviously we would need the 14-day pass, but if we activate it upon arrival, it would be valid until the 27th, so one day short of our return. Would you suggest we purchase a one-way train/metro ride to our hotel upon arrival and only activate the pass on the 2nd day?
I've read that there are regional trains, metro's and busses - but does the JRpass cover everything or do we need to purchase additional transportation locally?
Would appreciate any suggestions and info to make our journey most efficient!

Thank you!