Engine vibration on ignition circuit A

Hi. We have excactly same problem. 912ULS engine. We have repaired ignition modules at: www.carmo.nl.  We have swaped /adjusted carbs from another engine, new sparkplugs. Still the same. Maybe some of ignition coils is defective. The problem dissapears when engine is well heated up.

If the only thing that changes from your "smooth-running" state to the "rough-running" state is turning off one of the ignition circuits, I would argue that you definitely have an ignition issue - you just haven't found it yet. Neither fuel delivery nor air delivery is effected by turning off one of the ignition circuits, and it's those three things that work together to produce power...  

As Kevin alluded to, I would swap the ignition modules to see if it follows the module.  If not, it's most likely to be downstream from the module (plugs, plug caps, and wires, which I would check in that order - easiest to hardest to check). 

Of course, it is possible that the pickup points on the flywheel are out of spec, but that would seem to be low odds to me, and I would definitely check the other things first.  But it pretty much HAS to be in the ignition side of things, given what you're telling us.