I think you need to forget about passive arm for what you want to do... if you've got a fob with left and right buttons then it's a System 3. It will passive arm in full protection state, so you need to use 'service mode'.
In case you don't have your user guide - disarm the alarm as normal, turn on the ignition, hold down the RIGHT button until it beeps (about 5 seconds). The LED will stay lit and the alarm will beep every 20ish seconds. The bike is now completely separated from the alarm.
To come out of service mode, just press the right button.
Threaded Mode