I'd suggest going in May instead of April. The reason is because of the Sanja Matsuri. It's a summer festival at Asakusa, Tokyo.
The festival's pretty cool, Shrine Maidens, Kimonos, Yakuza showing off their tattoos, etc.
For anime/manga stuff, In Akihabara there's a store called Mandarake (Tall Black building). It's all 2nd hand but they're in really good condition and you can find stuff for almost 80% less then what you'd have to pay in regular stores.
There's a cafe called Good Smile Cafe on the 5th floor of Akiba Zone. They have menus and themes that revolve around certain anime series. When I went it was Hataraku Maou-sama and Oreimo.
If you want shopping and stuff, Shibuya is alright. I didn't go for shopping but thats where my friends went to
Also go to Roppongi, they have some pretty nice bars there. There's also the Mori towers in Roppongi, I remember it's like 1,500 yen for a ticket up. It's a pretty nice view and there's a cafe bar type of thing there as well. The top floor's a circle that leads you back to the elevator and they won't let you backtrack.
Have fun, I spent over a month there with some friends in the summer. If you want I can pm you some other cool places and other misc stuff.
This post was edited by Yinnyiin on Jan 10 2014 06:27am