Try booting from an usb (with a live linux image) stick and see if you can access your drive.

I have found this app. Didn’t test it but you might try it. https://github.com/maforn/TimedShutdownAndroid

On a rooted device or with adb you can execute the command:

sleep 60m && reboot -p

I have tried a yubikey on ubuntu without any problems. Could you please describe what exactly isn’t working