You're using a fairly low precision gearbox with low precision motors... You're going to have a lot of chatter, no matter how you make it run. If you re-machine your bearing plates to correct tolerance (AM does a good job for the number they make, don't get me wrong), you'll eliminate a lot of this...

However, most spur gear drive trains will make more noise when going slow then when going fast, due to the chatter of the gears. If you absolutely SOAK your gears in lithium grease, you'll lose a lot of the noise... but otherwise you're stuck with it.