Engine runs rough on one line

I doubt that the problem is with the plugs or the connectors on an engine that new. It is also unlikely to be the ignition modules with the symptoms that you describe. Odd though it sounds, I would be more suspicious of the fuel. In particular the tiny drill holes in the venturi can get blocked. I've had this happen and I had to clean them out very carefully using a can of carb cleaner and some compressed air.

Thank you for your feedback. However, I had my carburetors completely rebuilt about 50 hours ago. Based on my reasoning, if it were something to do with the fuel supply or carburetors, then the engine would actually have to run rough on both lines. I'm not switching off a carburetor line, just an ignition circuit—or am I wrong?

How do they compare at idle? I agree the problem is electrical, my money is on a spark plug.

Idle is simmilar but very hard to measure as a feeling, because on Idle it drops above 1600 rpm and if I switch off one line it becoms to low and the engine is not running smooth anyway. I hope I have time to install my new plugs, then I know more ;-) 

Spark plugs usually misfire at light loads as you are experiencing. The high-tension side i.e. plug leads usually show up under heavier loads.

Try changing spark plugs first.