Im no programmer, im just a random guy who wanted to help make a clear guide for people but I will try to help.
You generated the firmware file properly
you prepared your CF card, formatting it as per the instructions (first on computer as NTFS, then on camera)
Place the firmware file on the CF card
Put CF card in camera
Firmware update in camera menu
WHEN CAMERA IS DONE turn off and take out CF card, plug the CF card into your computer
Run EOSutility as per the instructions.
IF that does not work tell us the files on your card, maybe we can spot something there?