Yes, just remove the red wire from the connector as you need the signal and ground to remain connected. There's a little plastic tab on the back of the connector that you lift slightly and the cable and pin should then just slide out.
I've been reading up on failsafe and power module settings, (a lot more to read through though )
It looks like there could be a problem with your failsafe settings. As a 3S battery has a nominal voltage of 11.1V it shouldn't be entering failsafe at 11.4V which seems much too high, (this could explain your why you're getting a 'low voltage' failure).
The APM will enter (voltage) failsafe when either of the following conditions are met;
- Voltage drop below LOW_VOLT for more than 10 seconds.
- Your flight uses more than 80% of its capacity.
What voltage have you set your LOW_VOLT to?
and what have you set your BATT_CAPACITY to?
I'd recommend 10.5 for the low_voltage_cut_off, and although I'm tending toward the voltage setting, it won't hurt to check that the BATT_CAPACITY is set to 3000 (mAh)