Your Neon is OBDII so the scan tool will work. If you have a current problem that the computer detects it will set the CEL lite. Even if everything is good to go you should get a code 55 (end of codes) and usually a code 12 (battery disconnect within 50 start cycles).

Is the miss intermittent or does a specific cylinder drop out? Figuring that out will help a lot. Can you put on the emergency brake and block the tires so that you can load the engine and duplicate the miss at rest?

Master, again and still