. . . it isn't the wires coming through the lift gate. All those wires are fine.
How were the wires in the flexible boot checked? There's been cases where one or more of the wires inside the wrapped bundle was broken. These breaks are not apparent when simply lifting the rubber boot to inspect the exposed wires. Other than continuity testing, either the bundle has to be separated to inspect the wires, or each wire can be pulled at both ends to see if it (a broken wire) comes out of the bundle.
In any event, checking with a meter for power to the actuator connector at the latch will verify if the connections are good or if the actuator itself is faulty. (Note, when the keyless entry fob is pressed for lock or unlock, power is sent to the actuator for only about 2 seconds. So the meter will more likely only indicate a short pulse of voltage.)
. . . I was able to manually lock the left gate by taking the panel off the lift gate and manually locking the latch. Unfortunately it seemed to set off the door alarm. It wouldn't stop dinging.
Was the hatch fully closed when the lever was used to lock the latch? Did the dinging start as soon as the lever was set to the locked position or at some later time? If some time later, can you recall the situation, e.g. was it when a side door was opened? Did you try moving the lever back to the unlocked position to see if the dinging stopped?
As far as I know, manually locking the rear gate (hatch) latch from the inside should not cause "dinging", which is more often related to the key being left in the ignition switch when the driver door is opened or when a front seat is occupied but the seat belt isn't fastened.
Strangely enough there's a cheat code to fix this.
That procedure is for stopping the seatbelt warning: See:
http://www.subaruoutback.org/forums.../forums/66-problems-maintenance/147849-stop-seatbelt-dinging-outback-wagon.html