First time to Japan – first estimate at an itinerary

I thought id come here to ask the experts! me and my girlfriend are going to Japan for the first time in February for 11 nights. I have a basic idea but i will have definitely missed quite a lot im sure! Also need a couple more ideas for Tokyo. Sorry in advance for the way its written. We are getting the 7 day JR pass starting from the 5th day for ease.

Tokyo 1 –

* Arrive early (pickup all bits for trip at airport)
* Get to hotel in Ginza
* Nihonbashi Pokemon cafe
* **Not sure what area to head for or to move a day around later?**

Tokyo 2 –

* Meiji Jingu
* Yogogi park
* Togo shrine
* Mipig cafe Harajuku
* Shibuya & Crossing
* Pokemon center shibuya
* Over to shinjuku for dinner (omoide yokocho/golden gai)
* Karaoke bar in shinjuku

Tokyo 3 –

Whole day pretty much blocked out for Disneyland

Tokyo 4 –

* Senso Ji Temple
* Kasamise shopping street
* Walk sumida river
* Tokyo sky tree
* Akihabara area

Tokyo 5 – Hakone (no order for this yet)

* Heiwa no tori gate
* hakone shrine
* pirate ship across lake ashi
* **(considering mishima sky walk as it looks really cool but dont know how easy it is to get to)**

Kyoto 1 –

* Bullet train from Shinjuku (staying near Nijo castle)
* Gion district (all main temples on route) and Shijo avenue
* **Is there many restaurants around Gion district or is it better to come back towards the main part of city?**

Kyoto 2 –

* Train to arishiyama
* Bamboo forest
* Tenryu-ji temple
* Tegetsu-kyo bridge
* Monkey park
* Back to Kyoto for evening

Kyoto 3 –

* Fushimi Inara Taisha
* Nijo Castle
* Kyoto imperial palace

Osaka 1 – staying near Dotonbori

* Early train to Osaka
* Day blocked out for Universal studios
* Out in Dotonbori area

Osaka 2 – Nara Daytrip

* Lots of temples/shrines on route to Todai Ji +bell tower
* Kasuga Taisha
* Feeding the deer of course and relax for a few hours
* Back to Osaka for dinner

Osaka – Tokyo –

* **Any ideas of what to see in Osaka main city?**
* Bullet train back to Tokyo
* Team labs Planets
* **Any other ideas?**

Tokyo –

Flight back : 13:15