My tip for what to see in Tokyo is to go to Kyoto instead. Tokyo does have some wonderful things to see, but to me, Kyoto is a thousand times better for sightseeing. I'd want to live in Tokyo but visit Kyoto. And if you can time it during Sakura (cherry blossom) season or the changing of the leaves, even better. I see that you have Kyoto on your list. Spend at least a few days there. Kiyomizu temple, Kinkakuji (the golden temple), Ginkaku-ji (Silver temple), Gion, somewhere for a traditional meal, and so many other great things there.
The most amazing thing about Tokyo is simply the scale of it. Going somewhere that gives you a view (Skytree is probably the most popular, but I believe it is expensive and there can be long lines) is important. Then you can hit the Meiji Shrine, maybe see the Karajuku kids if that interests you, go to the Imperial gardens, stroll the streets of Asakusa, and whatever else floats your boat.
In both places, you can get by just fine with English. There might be some adventures in eating if you go to smaller, off the beaten path restaurants, but I had some amazing food experiences by asking the waiter his favorite and seeing what showed up. If you have a smartphone, download a translator app that doesn't need data.
Also, the Japanese people are amazingly thoughtful and kind. If you need help, ask. If the person can't help you or doesn't speak English, they will often guide you to a booth, a koban (police box) or some other place where you can get the info you need.