Advice on this itinerary

We need some help about this itinerary. We are buying JR Pass here in the US. we are not interested in Hirishima or Nagasaki but don't know if we are missing something in the south. Also if we are missing something that is worth sseing and can change with the idea that we have.

March 16th, Arrive at Tokyo (Narita) at 6:00pm.
March 17th, Stay all day in Tokyo (lots to see).
March 18th, trip to Nikko (maybe stay there or come back to Tokyo).
March 19th, (our anniversary) trip to Matsumoto castle and stay that night there.
March 20th, trip to Takayama and probably if time let us do it visit: Ogimachi, Suganuma and Ainokura. Stay in Takayama
March 21, trip to Kanazawa...maybe...
March 22, Bullet train to Kyoto
March 23: Kyoto
March 24th, Bullet train to Himeji and back to Kyoto
March 25th,(my birthday) Kyoto
March 26, Trip to Nara and Uji. Staying at Nara
March 27th, trip to Hakone and night there
March 28th, Back to Tokyo
March 29th, Tokyo and go to airport at 3:50pm... :-(

March 20th, trip to Takayama and probably if time let us do it visit: Ogimachi, Suganuma and Ainokura. Stay in Takayama

No, you won't have time to go to Ogimachi/Ainokura on that day, but you might do so on your way from Takayama to Kanazawa, although you won't have much time if you are staying only one night each in Takayama and Kanazawa.

March 22, Bullet train to Kyoto

Kanazawa to Kyoto is served by a regular train rather than a bullet train.

I don't see where you could insert an additional destination, but if you can make some additional time, here is a list of destinations to consider:
http://www.japan-guide.com/e/e623a.html