Did you match your firmware with the kernel you are using ?
One can experience weird errors if these do not match incl. segfaults.
More likely however it seems that some of your files are corrupted.
Easiest way to check this, grab an update.zip and unpack the KoboRoot.tgz or KoboRoot.img
In the unpacked directory:
find . -type f -exec sha256sum {} \; > sha256sums.txt
Copy the file to your kobo via nc ssh or whatever is working.
sha256sum -c /tmp/sha256sums.txt |grep -v "OK$"
Replace all files that end on FAILED. If you find a file that is corrupted, rename it.
So it occupies the corrupted space and it cannot be reused.
Really enjoying this topic, and to think i took you for a novice.