A modeler found a letter in the second-hand model he had bought, which states this with regard to the engine not running smoothly:
"Turn your engine upsidedown. Hook up some test clips and put power on your model. If you hear some very obvious rattling sounds, the universal coupling between the motor and gearbox is out of alignment. The fix is easy. Locate the brass plate with three screws, just above the rear drivers set. The rear-most screw is the culprit. Simply turn the screw slightly to the right or left until the noise disappears. When you have found the optimum setting where the engine runs very quiet and smooth, put a drop of locktite or ACC type glue on the head of the screw to keep it in place. That should do it."

If you have problems with the gears, here is a photo of the NorthWest Short Line replacement gear, part #2285-6.