In Kyoto, there is the international manga museum Google Maps They have a manga storyteller. I went with my husband (Japanese) and he loved it because there are literally tens of thousands to read. There are few exhibits and many, many manga. It’s close to Karasuma Oike station.
The Absolute Beginners Book Club is probably the best place to find the manga and novel list, especially as it has vocabulary lists etc for the chapters. I’ve read a few from there and like the choices they’ve made. The current manga is 俺物語! ・ My Love Story! 🍰 (Absolute Beginner Book Club) - #43 by ChristopherFritz
My favorite bookstore in Kyoto is Maruzen, which is huge and has a variety of book types, including manga (though it’s not walking distance). Google Maps It’s the two basement floors of a department store, fairly close to Shijo Kawaramachi, in an area with a lot of shopping. Also, BOOK OFF is a used bookstore chain that has manga, as well as bundles of series (many locations).
(Edited for clarification after checking OP’s location in Kyoto and to add the link to the book club).