this may or may not help but check the 2 screws that hold the 3 cylinder block assembly to the engine if they loosen up they create issues. if loose put a dab of locktite on threads keeps them snug yet removeable. other than that watch reciprocating areas and see if something is not right also as a heads up the 3 cylinder block crank has a weak area unsupported where brass gear meshes with motor gear under boiler shell mine broke in 2 but thanks to lionel reissuing them in legacy a year ago I was able to buy that assembly and my shay lives again.
good luck hope some or all helps