If the cogging is more pronounced than other similar sized Mabuchi motors, I doubt you're going to fix this without replacing the motor. The good news is, the Mabuchi 3.xx series motors are mostly all close to the same size and have the same shaft size and mounting hole spacing.
The MTH locomotive has much better gearing, usually around 16:1.
While the tall gear ratio might cause some issues, you should be able to get smooth operation at any speed step with the right motor.
