so does checking for errors with an led mean you used a noid light on the injector connectors??? if so and the injector wiring is most likeley fine.. when your having the misfire issue pull each plug wire or injector connector one at a time until the one you pull doesnt change how the car runs.. that would be the cylinder you want to focus on and can switch that injector with another to see if the problem switches to the other cylinder...
if you didnt test with a noid light you could also have issues with the wiring/connector...
good luck