11.7v li-po? No such thing, I assume you mean 11.1v li-po in which case you shouldn't use that with a stock CA, you'll rape that gearbox with that battery.
But about the motor, you're just installing the motor wrong, wires are getting pinched between the inside of the pistol grip and the motor which is why it seems like its hard to get in there, and the clicking is because the motor is jammed to far up in there and can't turn the gears over.