Hello from Tokyo. I sadly have not been to most of the places you listed, but I'll add what I can.
As Spinach said, Tokyo is too big to rec anything without knowing what you would like.
Akihabara is nice because Animate and Toranoana and random figure stores and things. The maids on the street advertising their cafe is a strange sight. (I personally rec Schatzkiste, if you like maids that aren't as ridiculous. Very quiet, nice place to sit and have tea for a moment.)
Akihabara is also great for recognizing sights you see in anime that took place there, like Oreimo or Stens;gate.
The other otaku cities are Nakano and Ikebukuro.
Nakano also has some old game/figure/dojin shops on the north side of the station, Nakano Broadway. Has a different atmosphere from Akihabara.
Ikebukuro is famous for having otaku content targeted at women. Like butler cafes.
Can I say "Hyogo (prefecture) is where Kobe (city) is" without sounding too mean?
If you're going to other parts of Hyogo too, I'll cautiously rec Himeji castle. I hear other castles, like Osaka and Nagoya, have elevators and relatively modern interior that makes them just glorified buildings that look like castles, but Himeji castle is preserved rather well, with minor additions like rails on stairs to keep visitors safer.
They finished a big repair a few years ago, so things may be different from when I last went.
If you like wagashi, a local one called Tamatsubaki is even liked by locals, not just for souvenir purposes.
My sister went to Hiroshima on a school trip. She said Miyajima/Itsukushima Shrine was really nice, though this is really basic so you probably know anyway.
If you're going to the nuclear bomb related places in Hiroshima, this manga based on the author's grandmother's experience might add to your visit.
Edit: there probably is someone writing the same info in English somewhere too, but this tweet has a handy map attached for TM related places
Spinach is so thorough, I feel mine is very poor compared to his. Feel free to ask questions if anything is unclear. I hope you enjoy your stay!