I would take a look at all your boots and make sure they aren't damaged on the inside where the boot connects to the plug. Check your coil pack connections and makes sure they are good as well. Here is some info on the coil packs.
I would think the ECU could try to adjust the tune to whatever signal is being sent, so the handheld tuner fakes the signal so the ECU thinks everything is hunky-dory. MIL ellimitaors do the same thing.:good:
Try unpluging the alternator. It sounds dumb but the alternator sends out a frequence when it goes bad and this frequency will interfere with your cam positioning sensor which will cause a back fire. And just because its still charging the battery doesn't mean its not going bad. Keep us posted on how it goes!