Glad you found the problem. I would just run it normally and regularly a couple of times per week. Make sure to vary the speed and direction so that the gears wear in over a wide range of service conditions. I second Breezinup's suggestion of an AC Commander. A fellow named Mossback Mike has been posting about some tests of AC-motored locomotives. He's documented that the usable voltage range is pretty narrow, so along with a proper break-in, having more speed steps (and setting the stall correctly) will get you better performance.
Mike's conventionally-controlled 2333 F3 managed to throttle down to 5 scale MPH. That's about as good as any can-motored loco can do!
