First thing I would do is check the valve adjustment. They may all work and appear the same but adjustment may be off. I can send you a Service Manual for your engine IF you like. Address below, put in proper format and remind me, engine model number and what you want
I suspect your problem is with the dual barrel carb.? Check to see if you may have lost one of the bushings for one of the main needle fuel valves. I have seen this before.
One cylinder is being starve of gas, while the other is getting plenty. Hence this is why you are not finding any electrical problems. You stated you cleaned the carb... I think you may have lost this easy to loose part... and did not notice it.