First time to Japan, 11 days itinerary

Hi everyone,
I'm going to Japan for our first time from Aug 19 to Aug 31.
This is my plan:
Could you give me some advice? Is my plan practical?
Thank you very much! :)

Day 1
Arrive Haneda airport at 3:30pm, go to airbnb near SHINJUKU station.
Day 2
Meiji Jingu - Takeshita Street - Harajuku shopping street - Shinjuku Gyoen National Garden - Golden Gai - Omoide Yokocho - Kabukicho Ichibangai
Day 3
Roppongi Hills - TV Asahi - Tokyo Tower - One Piece Tower Tokyo - Rainbow Bridge
Day 4
Ghibli Museum OR Skytree
Day 5
Tsukiji market - Ginza - Seimon Ironbridge - Chidorigafunchi Park - Imperial Palace - Yurakucho Chiyoda
Day 6 Leave Tokyo in the morning to Kyoto
Nijo Castle - Kyoto Imperial Palace - Heian Shrine - Yasaka Shrine - Ninenzake
Day 7
Nara park and near temples
Day 8
Arashiyama Bamboo Grove - Monkey Park - Tenryu ji - Toei Kyoto Studio Park and surroundings
Day 9 Leave Kyoto in the morning to Nagoya
Toyota Commemorative Museum of Industry and Technology - Nagoya Castle - Nagoya TV tower - Oasis 21
Day 10
Atsuta Shrine - Osu shopping district & Osu Kannon Temple
Going back to Tokyo in the evening
Day 11
Akihabara - Ueno park
Day 12
Senso ji or Skytree
Flight leave at 5:50pm

Looks ok to me.

For Ghibli you will need to buy tickets upfront. Look at the Ghibli page where it is explained. They can sell out within hours of becoming available.
For Skytree you can also reserve tickets upfront.

Enjoy your trip to Japan!

You might not get to everything in Day 6. You'll be traveling to Kyoto and checking in to your hotel or putting your luggage in a locker in the morning. Nijo Castle took me all afternoon when I was there in November 2017, but I rented the audio guide of the Castle and then walked leisurely through the gardens.

I think day 6 might be doable. But... You need to leave on a very early shinkansen to Kyoto, say the first 6:30am one. By the time you arrive at Kyoto and get moving onto your sightseeing, it will be after 10am. Baggage needs to go some, if hotel, drop off if they allow, if airbnb, then need to find enough lockers for your group.

If you arrive at lunch time, there is no way you'll achieve seeing all those locations. So I'd start on the one you wanna see the most, then move on to the others until you run out of light for the day.

Thank you sooooo much for the advices! :)
I will modify the plan for day 6.