Opinion on my itinerary

Hi, i'll be visiting Japan for 2-week honeymoon with my wife in the end of June.
For now i have made the following itenary, if someone can recommend to add/remove something, please say :).
First week - staying at Tokyo
1. Tokyo - National museum, Meiji shrine, Miraikan, Senso-ji, Tokyo municipality building, Akihabara and few other things.
2. Nikko.
3. Kamakura.
4. Saitama - Railway museum :)

Second week - staying at Kyoto
1. Himeji (castle) or Tsuyama (castle)
2. Koyosan. - whole day
3. Nara. - whole day
4. Kyoto - 2 days. International manga museum, Sento imperial palace (confirmed visit), Kamagimo shrine, Kinkaku-ji, Nishiki market, Higashiyma, Steam locomotive museum :), Fushimi Inari shrine.

Thanks in advance for any advices.

Oh you like trains!
I been to the Train Museum, you will love it!

Seems like a good pace that you have so far.

Suggestions:
Mt Fuji - Kawaguchi(My favorite) or Hakone
When you do Kamakura, should also look at Enoshima http://www.japan-guide.com/e/e3117.html or stopping at Yokohama for lunch in Chinatown.
Stopping at Kobe for Kobe Beef lunch. Make sure you get there before 1030am! Last time we got there at 1030am and it was almost 1230pm before we got in! Most places stop at 2pm. So yummy!

Hope this helps!
Have fun!

Thanks for the tips.
Definitely will visit Enoshima, looks great in the linked article.