With a new coil, wires and plugs it must be an issue with the control circuit for those two cylinders. You obviously checked for power at the coil but did you check the integrity of the control circuit? If you had an issue with the power wire to the coil you would have no spark in any cylinder and a primary ignition circuit failure for both coils in the pack.
You need to check the integrity of the black/green and black/orange wire between the PCM and the coil. Also, try disconnecting your alternator and any aftermarket electrical devices and see if you still have this problem.... Resistance should be virtually nothing, no continuity to ground and no continuity to power.
Likely your issue isn't related to RFI from the alt or a cell charger because usually RFI just messes with the PCM's ability to monitor the ignition control and not it's actual ability to deliver a good spark. If you have no spark you likely have a real issue, not RFI.
Either way, the PCM grounds the black/green wire to soak the primary coil for cylinders 1/4 and the black/orange for 2/3.