design-wise, the Atlas SW units and their driveline are very quiet runners. if you've already serviced the wheelsets, then it's time to open her up.
I'd check for a loose motor mount, or loose or unbalanced flywheel. also check the universals that connect the motor to the gear towers for binding.
I've also owned a Sunset 44 ton engine. The Atlas unit runs smoother in my opinion.
good luck.