It sounds like the motor is working.
I haven't had the opportunity to remove one of these window motors, but older Ford motors have three little nylon bushings that act as shock absorbers for the motor. When they wear out, the motor will make a clicking sound. It sounds like a gear is stripped.
On the older motors, you can buy a rebuld kit. The only thing that you really need to replace are the bushings though.
You have to remove the motor to rebuild it, just the same as if you were replacing the whole thing.