Basic principle to live "KISS" KEEP IT SIMPLE STUPID some times we over think problems and make them more difficult then they are. If you have a bad PCM and it is quit possible that the tuner even though you put it back stock, could have corrupted your stock codes that what it sounds like, IOM. I do this to myself sometimes on a daily basis, electrical problems I jump the gun and go digging when always the first step is battery and charging first then go from there. You did all the test for mechanical faliure but, if the PCM or ECU has corrupt parameters you will drive yourself mad. I hope your still covered under some sort of warranty because those aren't cheap. Keep us posted. we'll get you through this. Just take a step back take big hit of.. oh I mean take a deep breath and relax.