Wow again - all great advice, especially about pinpointing the anime. She will want to see the Pokémon store for nostalgia (she's "moved on"). Absolute top favorite in Anime is Hetalia. Not as sure about manga, as she reads whatever she finds at the library. I understand the manga will be mostly in Japanese anyway, so she's better off buying that here. She has done some cosplay at a couple of "cons", so that may be of interest, too. The division of "boy" and "girl" districts is really helpful. I will make sure she connects with the guide in advance to make sure it is all geared towards her interests. I also know some of the genre can be quite sexual and/or violent, so would want to steer away from that.
I do know about cat and other cafes - daughter is very interested, husband is not, so I guess I draw the straw on going to one of those. Was most interested to learn of hedgehog café!
Great to know we can self-guide a lot of the way - I tend to glaze over with a guide, and we do like to slow down/speed up at our own pace(s). Especially nice for Koya-san which just seems like a wonderful pause in a busy itinerary - wish we had time to spend more than a day...
Still unsure about laundry/Takkyubin - sounds a bit complicated, but will look at the itinerary and see. I think we'll just do our best and wash stuff in the sink if necessary!
I will most certainly be writing up a trip report to pay back/forward. Thanks again for all the great advice.