The engines are not balanced so when the flywheel spins slower it shakes the engine more. The faster you spin it, the smoother it becomes, to a point.
It also has to do with the 45 degree engine using a common crank pin. In this design the flywheel rotates 405 degrees and fires a plug, then it rotates 315 degrees and fires a plug, then 405 degrees again, then 315 and so on. At a low RPM, the difference in rotation distance is more noticable, hense the sound that a Harley makes. After the flywheel turns 405 degrees it is technically turning slower when the plug fires as opposed to the 315 degrees and then firing the plug. This means every other plug firing is to a slower flywheel and this contributes to the vibration of the engine.
Add all those factors add up and you get the "rough" idle I think you are talking about.
The TC88-B engines have counter balancers in them that spin offset weights to counter the flywheel weight. When the flywheels are "throwing" weight forward, the counter balancers are throwing weight backwards nullifying the vibrations. In basic terms.
