I can't really comment on changing to ext on user partition. I think I tried it as an experiment in the past, but as I didn't have a real need to do it or otherwise run the ext drivers under Windows, I haven't kept it up. If frostschutz's installer doesn't work, it will be because it was written a long time after the firmware version you are using
But, the problem you are having has been fixed in later firmware. In the version you are using, all cover images are stored in one directory one either the internal card, or the SD card, depending on where the book is. This causes a problem due to the fact the partition in use is formatted as FAT32 and the long file names. This means that covers for somewhere between 2000 and 3000 books can be stored.
With firmware version 2.9.0, Kobo changed to using a tree structure for the cover images and a hash based on the name to locate cover files. This solved the problem with using a FAT32 partition.
There are some other things you can do. Simply deleting all the cover images when the directory gets full will help a lot. They will be regenerated as needed, but it pushes the problem back for a while. And, unless you are scrolling through the whole library list, you will be removing covers images for books you don't see.
Another hack is to fiddle with the database and add a slash into the ImageID for your books. I did some experimenting before Kobo changed the cover image storage and the firmware will support sub-directories. The ImageID is in the database and is just the name of the cover image file. If it contains a slash, the firmware treats this as a directory hierarchy within the cover images directory. There was some discussion here about how to do this, but it was never implemented as Kobo solved the problem for us.
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