Three things I would do. When the engine is running rough, insert an inline spark tester between the coil and plug, to see if you are getting spark. If it is intermittent, or there is none, remove the kill wire from that coil and see if it changes. If it does, you know that something is grounding out that coil. If there is still not spark, the coil is bad. You if the spark is good, take a can of spray carb cleaner and spray around all of the intake gasket areas. If the engine speed changes, you will have found an air leak that is causing the problem and a gasket needs to be replaced.