Help with a Japan Itinerary

Hi All!
It's been 5 years since our last visit to Japan. This will be our 10 year anniversary. I'm so excited but I need help with an itinerary. My husband's job, once again, has limited us on the days again so I only have about 9 days to work with. we will be there 6/12-6/20 ( leaving at about 7:15 pm). The first trip we spent most of our time in Tokyo, so I wanted to get out and see more things this time. Mostly Kyoto. I've made out a list of things I want to see, but I'm unsure of of the days I should do they in. I will say I had planned to be in Kyoto the first 3 days. Also, our anniversary falls on the 15th and it would be nice to do something fun, romantic. Here is my list, maybe you you guys can help me out. Please keep in mind, anything can be crossed out, they are just on a list. Can you guys help and/ or give me your sample itinerary on what you would do? Also, should I purchase my rail passes before I head to Japan?
-Kyoto
-Nara ( deer)
-Bunny Island
-Disney Sea
-Universal
-Odaiba ( giant Gundam/ arcades)
-AKihabra
-Anima
---Gundam Cafe
---Eorozea
-Hakone
-Tokyo Tower
-Takoyami Museum
-Kareoke
-Zao Fox Village
-Cosplayers in Harajuku ( we missed them the last time we went. It was raining)

Thanks so much for all your time. I do appreciate it.

Zao as in Zao onsen? I think you might prefer Ginzan onsen over Zao Onsen. Better atmostphere.

Do take note that June is in the rainy season, so you might miss the peeps at Harajuku again.

For your special day, a nice dinner in Kyoto or Tokyo would be interesting.
Traditional Kaiseki Ryori in Kyoto Tower or along the Kamo River never fails to please.
For something simpler, there is always Kobe beef set meal.

You can only order JR Pass in your home country, so please do so.

Nara isn't the best place for Deer. If you are getting a JR Pass, do a day trip to Hiroshima's Miyajima. The deer there are friendler and I find the place to be more romantic, especially after the sunsets.
It is a pretty long train ride but can be done in a day if you set off early and leave late. Shinkansens are comfortable too so no worries there!

Bunnny island (Okunoshima is between Hiroshima and Okayama), requires a bit of a hassle to get there. Shinkanse, local train, ferry (about 7 a day). However, if you are staying in Hiroshima it is not too time consuming.

Currently it seems something like
12th
Tokyo Survive Jet Lag
Go about Akihabara or Shibuya for light shopping
13th
Go to Meiji Shrine
Go to Omotesando
Go to Harajuku
Shinkansen to Kyoto
Do Kiyomizudera
Walk through the old streets to Yasaka Shrine
Dinner around Teramachi dori or Gion depending on budget
See potoncho
14th
Cover Kinkakuji, Ninnanji, and Ryoanji in the morning
Cover Tenryuji, bamboo grove, and sagano romantic rail in the afternoon
Cover Kyoto city station for dinner
After sunset, go to Fushimi Inari for a mystical romantic experience

15th
Do the stroll from Silver Pavillion to Nanzenji. Pop by the eateries and small shops.
There is a very very good Japanese traditional snacks shop. Cover Heian Shrine. Cover Kamo Shrine. Walk along Kamo river at night.
The southern part of Kamo river has a couple of restaurants by the river. There are countless restuarants to enjoy a quiet and yummy dinner.

16th
Go to Osaka in the morning, visit Universal Studios.
Leave your luggage at the train station locker.
Collect it after your day of fun. Take a train to anywhere nearer to Hiroshima.
E.g.
Kobe
Himeji
Okayama
Mihama

17th
Bunny Island in the day
Miyajima at night
Hiroshima itself is known for Okonomiyaki and the atomic bomb museum. Isn't all that romantic though

18th
Morning back to Tokyo
May want to see the bomb museum?
Or can go back to Tokyo later in the day, spending some time (3-4 hours) in Okayama's garden or Himeji's castle.

19th-20th
DisneySEA and home flight

Required 7 day JR Pass

If you aren't too into deer, can forgo the beautiful night view at Miyajima, and the bunny island; you could spend more time in Osaka/Kyoto or maybe go places like Nikko/Kamakura/Nagano/Kanazawa.

Hmm. some good points in here. some things we have already seen as well. so I will take this into consideration.
thanks so much for the help. As far as the Zao fox village, I had only head of this one http://en.japantravel.com/view/zao-fox-village.
I doubt I will be allowed in any onsen since I have tattoos and I know that is still taboo in some areas.

Zao fox village is pretty out of the way, to not go to an onsen or stay overnight at that atmospheric town seems a waste to me.

Unless really noticeable, you can cover your tattoos with towel or go during wee hours