If you have switched the cylinders, and the problem remains on #3, then you may have a faulty fuel injector. Unplug the electrical connector to injector #3 and take an Ohms reading. The resistance value should be 1.95 - 2.3 ohms at room temperature.
You swapped injectors? I though you meant you swapped plug wires (its the easier of the 2 to swap) Sorry. Next step is to check for spark coming out of the coil pack for cylinder #3. With the engine running, remove the spark plug wire and see if there is spark jumping.
Very common for these coils to go bad. Its a nice, easy fix. Have a great day.