Um, what? I really made this as simple as I possibly could. All you have to do is follow all the directions.
Once RSD is finished flashing, the phone stays in AP Fastboot. At that point you're instructed to shut the phone off, hold volume up and down and press power, volume down to select recovery, volume up to select it, volume up and down when the android icon comes up, and then install the update from sdcard in recovery. Wipe the cache, reboot the phone, then when it's fully rebooted, optionally root if you so desire. So, I really don't know what exactly you're doing, but, it doesn't sound like the directions I give in the script.