I've created a makefile to automate the patching process on Linux. See
post #3: Automatic method.
You might need to install GNU make to use this, but once that is done and you have edited the conf file, running make will download the firmware, check that it is the correct firmware for the patch, extract the necessary file, compile the patching program, apply the patch, and create the KoboRoot.tgz file automatically. Then all you need to do is copy the resulting KoboRoot.tgz to the .kobo directory on your device.
Beware that the makefile doesn't check that your device is running the correct firmware, it is up to you to check that before you copy KoboRoot.tgz onto the device and eject.