Check the MRPI log (it's somewhere inside extensions/MR Installer) and you will have better idea what happens with each bin package you tried to install..
As for KOReader not working: if you download wrong version for your device + firmware combination then that would be the expected outcome.
You need to download and use
koreader-kindlepw2-v2025.10.zip if you have PW3 on fw <= 5.16.2.1.1.
https://github.com/koreader/koreader...2-v2025.10.zip
Also check the crash log file inside koreader folder after it failed to start when you run it.
KOReader should run and work as long as it can run as root user. If you "installed" / unpacked the correct version. If it doesn't chances are that you indeed have problems with jailbreak / the hotfix / "gandalf" binary in particular.