That sounds like linkage. Have you oiled it? Make sure you oil the valve guide slots under the valve guide where the valve linkage goes back and forth. loco must be lubed upside down to get the oil in this area.
Also oil where the piston goes into the steamchest, turn the wheels so the piston rod is fully extended back, then oil closest to the steam chest. Then the piston rod will push the oil into the steamchest opening it rides in.
Looking at my berk there are 13 points of motion on just one side of drive rods alone, that I lube
I'm not sure what " motor" you talking about but that certainly isn't the smoke unit motor and it sounds to slow and loud to be the can motor powering the loco.
It sounds rythmic like the linkage, as its almost in time with the chuff. Also make sure you lube the axle bushings between the back of each driver and the chassis.
Every moving point of the linkage needs a drop of oil whether or not the manual specifies each point.
FWIW I've found a "heavier" light oil like Labelle 102 works better for steamer linkage and O guage trains in general. Its stays where you put it and lasts longer.