Need help with 5 days in Tokyo Anniversary Trip

In October my wife and I will be spending 5 days in Tokyo for our 10th wedding anniversary. It'll be our first trip to Japan. We have booked a hotel in Akasaka for easy access to the different transit lines and a more relaxed vibe. So far all I have is a rough draft of the different areas.

Day 1: Shibuya, harajuku, meiji shrine, Shibuya sky

Day 2: ueno, Tokyo national museum, asakusa, sonsoji temple, Akihabara

Day 3:Shinjuku, shimokitazawa

Day4:yanesen, yanaka ginza

Day 5: Akasaka, hei jinja, kichijoji, koenji

I'm not sure if this seems overly ambitious on some days or if some of the areas could be grouped more efficiently. We usually love to explore when we travel. I plan on using tabelog to find places to eat wherever we happen to be. We are foodies, love coffee, vinyl, vintage and trendy clothing, books. We are really interested in anything unique to Tokyo that we can experience.

I really want to make this a special trip. Any help or recommendations for cool places to eat, shop, and explore would be greatly appreciated.

by ilovemeranda