You could try Giorgio's Koreader port, or Sergey's CoolReader port, both use the folder structure we are used to. I am using Koreader for my large collection arranged like you described on my external uSD card, and am increasingly pleased with it on my AuraHD. I have seen posts where Mini users are also able to use it. You can put your existing folders into a hidden folder, and avoid Kobo's lengthy and finicky processing.
https://www.mobileread.com/forums/sho...82&postcount=3
Luck;
Ken