You are talking about a Poke3, right?
Ok, put the decrypted, modified update.zip on a flash drive in the root directory as update.zip
Download p9mod.prc (and just rename it p9mod.img).
Flash it with "fastboot flash recovery p9mod.img" or EDL or dd it if you are rooted.
Reboot recovery
You will hear a "bong" of the ADB connecting. 4 seconds later the screen will turn white.
Code:
C:\>adb shell
# start autoupdate
It will say "Waiting for flash".
Unplug the cable that you are using for ADB.
Plug in your flash drive.
Sit back. (Please note if it mentions vfat or exfat.)
It should go to completion, then reboot.
For latest version see later posts...