Sweet! I went a few years ago with my partner and absolutely loved our time there.

In Tokyo, for nerd shit, I'd recommend checking out one of the Pokemon Centers, hitting up an arcade, and maybe checking out Artnia if you like Square Enix IPs. If you have a more niche interest, Tokyo may have something specific for you. I'm into Warhammer so checking out the Games Workshop store there was neat. For touristy stuff, going up in the Skytree is pretty awesome and can be cool to time at sunset if you bring sunglasses with you. If you don't want to pay for that, the Tokyo Metropolitan Gov't Building has an observation deck that isn't as tall, but it's free. I'm assuming you'll be doing the Shinkansen to Kyoto. You should definitely pick up some bentos from the train station before you go and eat them on the train. It's great. When you book your tickets for the train, try and be on the north-facing side. If the weather is clear enough, you can see Mt. Fuji on the way. I'd also recommend going to the Yodobashi in Akihabara and walking through there just to see a wide spread of things commonly sold in Japan. They have everything from PC parts to pens to home appliances.

Kyoto is a bit different than Tokyo. It's an older, quieter city, but still really interesting. It's common for people to wear kimono and walk the old districts. Mass transit is different there from what I recall. There are fewer subways (I believe they didn't want to bore underneath the very ancient temples) so I ended up walking more since buses are confusing to me and I wasn't there too long. If you have the time to spare and feel like a bit of a workout, I'd recommend climbing Mt. Inari. It's famous for the huge number of torii gates. There are some beautiful overlooks of Kyoto from the mountain on the way. I climbed it at night and the views of the city were fantastic. If you are looking for a new bag/backpack, check out Ichizawa Shinzaburo Hanpu. When I was there, they only sold locally in Kyoto, but it looks like you can order them online now. There are also some very old (and expensive) kitchen knife shops in the city.