Tokyo-Kyoto Itinerary

This is going to be my first time in Japan and I already have everything booked (flight and hotel) now I am working on building an itinerary. I am open to any suggestions but for the most part I am planning on walking between the different things I want to see since I've built this out to explore certain neighborhoods and be spontaneous along the way.

I am from NYC so I walk extensively pretty much everyday and I am also trying to learn some basic Japanese to be able to communicate with people. If there are any tips/suggestions and resources for learning Japanese I am open to it.

For food I am not looking for anything particular just looking for random food stalls, street food, restaurants, and bars along the way. Although I would like to do an Omakase night (any recommendations are helpful).

Day 0: 
Arrive to Tokyo November 17th at 14:30, check into hotel in Shinjuku
Walk through Shinjuku Gyeon and if I have time go to Meiji Jinju (12 minute walk from each other) 
Find dinner somewhere and go back to the hotel 

Day 1
Meiji Jinju Gaien (If I didnt have time Day 1) 
Walk through Shibuya Scramble 
Explore random streets and shops 

Day 2 
Tokyo Tower (40 min walk to Imperial Palace) 
Imperial Palace (30 min walk to Tsukiji Fish Market) 
Tsukiji Fish Market 

Day 3 
Tokyo SkyTree (25 min walk to Senso Ji) 
Senso Ji (10-15 min walk to Kappabashi) 
Kappabashi dougu street for shopping (45 min walk to Nezu Shrine) 
Nezu Shrine 

Day 4 
See what I didnt get a chance to see

Day 5
Check out of Hotel in Tokyo and head to Kyoto via Bullet Train 8am-10:30am 
Check into hotel or have them store my luggage until check in
Hotel is close to Kyoto Station so I should be able to get out into the city by 11 (hopefully)
Gio-ji Moss Garden (35 min walk to Okochi Sanso) 
Okochi Sanso  (Drive to Kinkakuji Temple about 30-40 mins) 
Kinkakuji Temple (35 min back to Kyoto Station) 

Day 1 Kyoto
Ruriko-In Temple (get there super early) 
Nishiki market shopping (1 hour by train to get here from Ruriko-In Temple) 
Go through the market and explore 
Imperial Palace (20 minute walk from Nishiki Market) 

Day 2 (these are relatively all in the same area)
Yasaka Pagoda
Sannenzaka Path
Kiyomizu-dera
Kodai-ji temple 
Explore Gion 

Day 3 
Day trip to Osaka 

Day 4 
Do whatever I didn't do / shopping 
Bishamondo Temple (might change this)

Day 5
Head back to Tokyo via Bullet Train 
Arrive at 12ish
Fly home at 16:30