this may or may not help your issue but check the 2 screws that hold the reciprocating cylinder and crankshaft assembly if they loosen up they allow the main motor gear to become unmeshed with each other. if this is your issue a little blue Loctite on both screws will cure that.
reason I mention it is this was a issue with the original tmcc 3 truck shays. as to the gears not meshing on the axels they have a sweet spot it takes some doing but once both axel ends are in the round holes they do line up and run fine afterwards.
hope this might help some of you